Groundwater Modeling System

Transcription

1 THE DEPARTMENT OF DEFENSE Groundwater Modeling System GMS v3.0 TUTORIALS

2

3 GMS 3.0 Tutorials Copyright 1999 Brigham Young University Environmental Modeling Research Laboratory All Rights Reserved Unauthorized duplication of the GMS software or user's manual is strictly prohibited. THE BRIGHAM YOUNG UNIVERSITY ENVIRONMENTAL MODELING RESEARCH LABORATORY MAKES NO WARRANTIES EITHER EXPRESS OR IMPLIED REGARDING THE PROGRAM GMS AND ITS FITNESS FOR ANY PARTICULAR PURPOSE OR THE VALIDITY OF THE INFORMATION CONTAINED IN THIS USER'S MANUAL The software GMS is a product of the Environmental Modeling Research Laboratory (EMRL) of Brigham Young University. Last Revision: November 17, 1999

4

5 TABLE OF CONTENTS 1 INTRODUCTION SUGGESTED ORDER OF COMPLETION RT3D TUTORIALS DEMO VS. NORMAL MODE SURFACE MODELING WITH TINS GETTING STARTED REQUIRED MODULES/INTERFACES IMPORTING VERTICES TRIANGULATING CONTOURING SHADING EDITING TINS DRAGGING VERTICES DRAGGING IN OBLIQUE VIEW USING THE EDIT WINDOW LOCKING VERTICES ADDING VERTICES DELETING VERTICES SMOOTHING A TIN Deleting the TIN Copying the Vertices Subdividing the TIN Interpolating the Elevations Deleting the Scatter Point Set READING ANOTHER TIN CHANGING THE ACTIVE TIN HIDING AND SHOWING TINS DELETING THE TINS CONCLUSION STRATIGRAPHY MODELING WITH SOLIDS GETTING STARTED REQUIRED MODULES/INTERFACES CONSTRUCTING THE SOLID MODELS READING BOREHOLE DATA CHANGING THE Z SCALE DISPLAYING THE HOLE NAMES CREATING AN EXTRAPOLATION POLYGON Setting Up the View Turning on the Drawing Grid Defining the Boundary Arc Creating the Polygon Turning off the Drawing Grid

6 vi GMS Tutorials 3.8 CONSTRUCTING THE GROUND SURFACE TIN Selecting the Contacts Creating the TIN Hiding the TIN CONSTRUCTING THE GREEN SEAM TIN Automatically Selecting Contacts Creating the TIN Hiding the TIN CONSTRUCTING THE RED SOIL TIN Constructing the TIN Hiding the TIN CONSTRUCTING THE BLUE SEAM TINS Constructing the Top TIN Constructing the Bottom TIN Hiding the TINs CONSTRUCTING THE RED SOLID Creating the Solid Shading the Solid CONSTRUCTING THE BLUE SEAM SUBTRACTING THE BLUE SEAM CONSTRUCTING THE GREEN SOLID CONSTRUCTING THE TOP BLUE SOLID VIEWING THE SOLIDS CROSS SECTIONS Creating the Cross Sections Hiding the Solids Deleting the Boreholes Deleting the Polygon Shading the Cross Sections LAYER BOUNDARIES DELETING THE SOLIDS AND TINS CONCLUSION D GEOSTATISTICS GETTING STARTED REQUIRED MODULES/INTERFACES IMPORTING A SCATTER POINT SET CHANGING THE DISPLAY OPTIONS CREATING A BOUNDING GRID SELECTING AN INTERPOLATION SCHEME LINEAR INTERPOLATION CONTOURING THE GRID MAPPING ELEVATIONS SHADING THE GRID CLOUGH-TOCHER INTERPOLATION SIMPLE IDW INTERPOLATION IDW INTERPOLATION WITH GRADIENT PLANES IDW INTERPOLATION WITH QUADRATIC NODAL FUNCTIONS TRUNCATION NATURAL NEIGHBOR INTERPOLATION KRIGING Creating the Experimental Variogram Creating the Model Variogram

7 Table of Contents vii Interpolating to the Grid SWITCHING DATA SETS USING THE DATA CALCULATOR DELETING ALL DATA CONCLUSION D GEOSTATISTICS GETTING STARTED REQUIRED MODULES/INTERFACES IMPORTING A SCATTER POINT SET DISPLAYING DATA COLORS Z MAGNIFICATION CREATING A BOUNDING GRID SIMPLE IDW INTERPOLATION DISPLAYING ISO-SURFACES INTERIOR EDGE REMOVAL FRINGE SPECIFIED RANGE USING THE Z SCALE OPTION IDW INTERPOLATION WITH GRADIENT PLANES IDW INTERPOLATION WITH QUADRATIC FUNCTIONS OTHER INTERPOLATION SCHEMES VIEWING THE PLUME WITH A CROSS SECTION USING THE TRUNCATION OPTION SETTING UP A MOVING CROSS SECTION FILM LOOP Display Options Setting up the Film Loop Playing Back the Film Loop SETTING UP A MOVING ISO-SURFACE FILM LOOP DELETING THE GRID AND SCATTER POINT DATA CONCLUSION MODFLOW - GRID APPROACH DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES CREATING THE GRID INITIALIZING THE MODFLOW SIMULATION THE BASIC PACKAGE Titles Packages Units The IBOUND Array Starting Heads Exiting the Dialog ASSIGNING IBOUND VALUES DIRECTLY TO CELLS Viewing the Left Column Selecting the Cells Changing the IBOUND Value Checking the Values THE BCF PACKAGE Layer Types Layer Parameters Top Layer

8 viii GMS Tutorials Middle Layer Bottom Layer THE RECHARGE PACKAGE THE DRAIN PACKAGE Selecting the Cells Assigning the Drains Assigning the Drain Elevations THE WELL PACKAGE Top Layer Wells Middle Layer Wells Bottom Layer Well SAVING THE SIMULATION RUNNING MODFLOW VIEWING THE SOLUTION Changing Layers Color Fill Contours Color Legend CONCLUSION MODFLOW - CONCEPTUAL MODEL APPROACH DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES IMPORTING THE BACKGROUND IMAGE Reading the Image Image File vs. TIFF File FEATURE OBJECTS BUILDING THE LOCAL SOURCE/SINK COVERAGE Defining the Units Defining the Boundary Copying the Boundary Defining the Specified Head Arcs Defining the Drain Arcs Building the polygons Creating the Wells DELINEATING THE RECHARGE ZONES Switching Coverages Creating the Landfill Boundary Building the Polygons Assigning the Recharge Values DEFINING THE HYDRAULIC CONDUCTIVITY Top Layer Bottom Layer LOCATING THE GRID FRAME CREATING THE GRID DEFINING THE ACTIVE/INACTIVE ZONES INITIALIZING THE MODFLOW DATA CONVERTING THE CONCEPTUAL MODEL INTERPOLATING LAYER ELEVATIONS Importing the Ground Surface Scatter Points Calculating a Starting Head Data Set Interpolating the Heads and Elevations Importing the Layer Elevation Scatter Points

9 Table of Contents ix Interpolating the Layer Elevations Adjusting the Display Viewing the Model Cross Sections Fixing the Elevation Arrays CHECKING THE SIMULATION SAVING THE PROJECT RUNNING MODFLOW VIEWING THE HEAD CONTOURS VIEWING THE WATER TABLE IN SIDE VIEW VIEWING THE FLOW BUDGET ADDING ANNOTATION CONCLUSION MODPATH DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES IMPORTING THE PROJECT INITIALIZING THE MODPATH SIMULATION ASSIGNING THE POROSITIES Assigning the Porosities to the Cells DEFINING THE STARTING LOCATIONS Selecting the Cell Creating the Starting Locations SPECIFYING THE TRACKING DIRECTION SAVING THE SIMULATION RUNNING MODPATH VIEWING THE SOLUTION Viewing the Pathlines in Cross Section View TRACKING PARTICLES FROM THE LANDFILL Changing the Tracking Direction Deleting the Starting Locations Defining the New Starting Locations SAVING THE SIMULATION RUNNING MODPATH VIEWING THE SOLUTION CONCLUSION MT3DMS GRID APPROACH DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES BUILDING THE FLOW MODEL Creating the Grid Initializing the MODFLOW Simulation The Basic Package The BCF Package Defining the Wells Saving the Simulation Running MODFLOW Viewing the Flow Solution BUILDING THE TRANSPORT MODEL Initializing the Simulation

10 x GMS Tutorials The Basic Transport Package The Advection Package The Dispersion Package The Source/Sink Mixing Package Saving the Simulation Running MT3DMS Reading in the Transport Solution Changing the Contouring Options Setting Up a Film Loop CONCLUSION MT3DMS CONCEPTUAL MODEL APPROACH DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES IMPORTING THE PROJECT INITIALIZING THE MT3DMS SIMULATION Defining the Units Defining the Species Defining the Stress Periods Selecting Output Control Selecting the Packages ASSIGNING THE AQUIFER PROPERTIES Assigning the Parameters to the Polygons ASSIGNING THE RECHARGE CONCENTRATION CONVERTING THE CONCEPTUAL MODEL LAYER THICKNESSES THE ADVECTION PACKAGE THE DISPERSION PACKAGE THE SOURCE/SINK MIXING PACKAGE DIALOG SAVING THE SIMULATION RUNNING MT3DMS VIEWING THE SOLUTION VIEWING A FILM LOOP MODELING SORPTION AND DECAY Turning on the Chemical Reactions Package Entering the Sorption and Biodegradation Data SAVING THE SIMULATION RUNNING MT3DMS VIEWING THE SOLUTION GENERATING A TIME HISTORY PLOT Creating an Observation Coverage Creating an Observation Point Creating a Time Series Plot Plotting Multiple Curves Moving the Observation Point CONCLUSION SEAM3D DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES IMPORTING THE FLOW MODEL

11 Table of Contents xi 11.5 INITIALIZING THE SEAM3D SIMULATION BASIC TRANSPORT PACKAGE Defining the Units Setting up the Stress Periods Package Selection Defining the Species Output Control Entering the Porosity Starting Concentrations ADVECTION PACKAGE DISPERSION PACKAGE SOURCE/SINK MIXING PACKAGE CHEMICAL REACTION PACKAGE NAPL DISSOLUTION PACKAGE Selecting the Cells Assigning the Concentration Entering the NAPL Data BIODEGRADATION PACKAGE Minimum Concentrations Electron Acceptor Coefficients Generation Coefficients Use Coefficients Saturation Constants Rates Starting Concentrations SAVING AND RUNNING THE SIMULATION READING THE SOLUTION SETTING THE CONTOURING OPTIONS VIEWING THE CONCENTRATION CONTOURS SETTING UP A TIME SERIES PLOT Moving the Observation Point Plotting Multiple Data Sets OTHER VIEWING OPTIONS CONCLUSION DEFINING LAYER DATA GETTING STARTED REQUIRED MODULES/INTERFACES USING THE "TRUE LAYER" MODE INTERPOLATING TO MODFLOW LAYERS SAMPLE PROBLEMS BUILDING THE GRID CASE 1 COMPLETE LAYERS Importing the Scatter Point Sets Interpolating the Elevation Values Viewing the Results CASE 2 EMBEDDED SEAM Importing the Scatter Points Interpolating the Values Correcting the Layer Data CASE 3 OUTCROPPING Importing the Points Interpolating the Values

12 xii GMS Tutorials Correcting the Layer Values CASE 4 BEDROCK TRUNCATION Importing the Scatter Points Interpolating the Values Viewing the Results Correcting the Layer Values Viewing the Corrected Layers CONCLUSION REGIONAL TO LOCAL MODEL CONVERSION DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES READING IN THE REGIONAL MODEL CONVERTING THE LAYER DATA TO A SCATTER POINT SET APPROACHES TO BUILDING THE LOCAL MODEL BUILDING THE LOCAL CONCEPTUAL MODEL Creating a New Coverage Creating the Boundary Arcs Building the Polygon Marking the Specified Head Arcs CREATING THE LOCAL MODFLOW MODEL Creating the Grid Activating the Cells Mapping the Attributes INTERPOLATING THE LAYER DATA SAVING AND RUNNING THE LOCAL MODEL VIEWING THE RESULTS CONCLUSION MODEL CALIBRATION DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES READING IN THE MODEL OBSERVATION DATA ENTERING OBSERVATION POINTS Creating an Observation Coverage Creating an Observation Point Calibration Target Point Statistics READING IN A SET OF OBSERVATION POINTS Deleting the Current Coverage Reading in the Points ENTERING THE OBSERVED STREAM FLUX GENERATING ERROR PLOTS Computed vs. Observed Plot Error Summary EDITING THE HYDRAULIC CONDUCTIVITY CONVERTING THE MODEL COMPUTING A SOLUTION Saving the Simulation Running MODFLOW

13 Table of Contents xiii READING IN THE SOLUTION ERROR VS. SIMULATION PLOT CONTINUING THE TRIAL AND ERROR CALIBRATION Changing Values vs. Changing Zones Viewing the Answer CONCLUSION FEMWATER FLOW MODEL DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES BUILDING THE CONCEPTUAL MODEL Importing the Background Image Initializing the FEMWATER Coverage Defining the Units Creating the Boundary Arcs Redistributing the Arc Vertices Defining the Boundary Conditions Building the Polygon Assigning the Recharge Creating the Wells BUILDING THE 3D MESH Defining the Materials Building the 2D Projection Mesh Building the TINs Importing and Interpolating the Terrain Data Importing and Interpolating the Layer Elevation Data Building the 3D Mesh HIDING OBJECTS CONVERTING THE CONCEPTUAL MODEL SELECTING THE ANALYSIS OPTIONS Entering the Run Options Setting the Iteration Parameters Selecting Output Control Defining the Fluid Properties DEFINING INITIAL CONDITIONS Creating the Scatter Point Set Creating the Data Set DEFINING THE MATERIAL PROPERTIES SAVING AND RUNNING THE MODEL VIEWING THE SOLUTION Viewing Fringes Viewing a Water Table Iso-Surface Draping the TIFF Image on the Ground Surface CONCLUSION SEEP2D - CONFINED DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES CREATING THE MESH Defining a Coordinate System Creating the Corner Nodes

14 xiv GMS Tutorials Interpolating Intermediate Nodes Creating an Extra Node Creating the Elements Deleting the Sheet Pile Element Refining the Mesh RENUMBERING THE MESH INITIALIZING THE SEEP2D SOLUTION SETTING THE ANALYSIS OPTIONS ASSIGNING MATERIAL PROPERTIES ASSIGNING BOUNDARY CONDITIONS Constant Head Boundaries SAVING THE SIMULATION RUNNING SEEP2D VIEWING THE SOLUTION CONCLUSION SEEP2D - UNCONFINED DESCRIPTION OF PROBLEM GETTING STARTED REQUIRED MODULES/INTERFACES CREATING THE MESH Defining a Coordinate System Creating a Coverage Creating the Corner Points Creating the Arcs Redistributing Vertices Creating the Polygons Assigning the Material Types Constructing the Mesh RENUMBERING THE MESH INITIALIZING THE SEEP2D SOLUTION SETTING THE ANALYSIS OPTIONS ASSIGNING MATERIAL PROPERTIES ASSIGNING BOUNDARY CONDITIONS Specified Head Boundary Conditions Exit Face Boundary Conditions SAVING THE SIMULATION RUNNING SEEP2D VIEWING THE SOLUTION MODELING FLOW IN THE UNSATURATED ZONE Reading in the Original Model Changing the Mesh Display Changing the Analysis Options Editing the Material Properties SAVING THE SIMULATION RUNNING SEEP2D VIEWING THE SOLUTION CONCLUSION

15 1 Introduction CHAPTER 1 Introduction This document contains tutorials for the Department of Defense Groundwater Modeling System (GMS). Each tutorial provides training on a specific component of GMS. Since the GMS interface contains a large number of options and commands, you are strongly encouraged to complete the tutorials before attempting to use GMS on a routine basis. In addition to this document, the GMS Reference Manual also describes the GMS interface. Typically, the most effective approach to learning GMS is to complete the tutorials before reading the reference manual. 1.1 Suggested Order Of Completion In most cases, the tutorials can be completed in any desired order. However, some of the tutorials are pre-requisites for other tutorials. For example, since TINs are used in the construction of solid models, the Surface Modeling With TINs tutorial (Chapter 2) should be completed before the Stratigraphy Modeling With Solids tutorial (Chapter 3). 1.2 RT3D Tutorials This document contains all of the tutorials for GMS except for the RT3D tutorials. Due to the large number of RT3D tutorials (one for each reaction package), they are contained in a separate document.

16 1-2 GMS Tutorials 1.3 Demo vs. Normal Mode The interface for GMS is divided into ten modules. Some of the modules contain interfaces to models such as MODFLOW. Such interfaces are typically contained within a single menu. Since some users may not require all of the modules or model interfaces provided in GMS, modules and model interfaces can be licensed individually. Modules and interfaces that have been licensed are enabled using the Register command in the File menu. The icons for the unlicensed modules or the menus for model interfaces are dimmed and cannot be accessed. GMS provides two modes of operation: demo and normal. In normal mode, the modules and interfaces you have licensed are undimmed and fully functional and the items you have not licensed are dimmed and inaccessible. In demo mode, all modules and interfaces are undimmed and functional regardless of which items have been licensed. However, all of the print and save commands are disabled. While some of the tutorials may be completed in either normal or demo mode, many of them can only be completed in normal mode. The required mode is discussed at the beginning of each tutorial. If the tutorial must be completed in normal mode, the modules and interfaces needed for the tutorial are listed. If some of the required items have not been licensed, you will need to obtain an updated password or hardware lock before you complete the tutorial.

17 2 Surface Modeling With TINs CHAPTER 2 Surface Modeling With TINs The TIN module in GMS is used for general-purpose surface modeling. TINs are formed by connecting a set of xyz points (scattered or gridded) with edges to form a network of triangles. The surface is assumed to vary linearly across each triangle. TINs can be used to represent the surface of a geologic unit or the surface defined by a mathematical function. TINs can be displayed in oblique view with hidden surfaces removed. Elevations or other values associated with TINs can be displayed with color fringes or contours. TINs are used in the construction of solid models and 3D finite element meshes. This tutorial should be completed before beginning the Stratigraphy Modeling with Solids tutorial. The emphasis in this tutorial is on the basic tools for editing TINs. A description of how TINs are used in the construction of solids is provided in the following tutorial. 2.1 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state. 2.2 Required Modules/Interfaces This tutorial can be completed in either demo mode or normal model. If you are already in demo mode, you may continue with the tutorial. If you are in normal mode, you will need to ensure that the necessary components have

18 2-2 GMS Tutorials been licensed. This tutorial utilizes the following components of the GMS interface: The TIN module The 2D Scatter Point module You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If each of these items is enabled, you can proceed to complete the tutorial in normal mode. If not, you will need to switch to demo mode before continuing. To switch to demo mode: 1. Select the Demo Mode command from the File menu. 2. Select OK at the prompts. 2.3 Importing Vertices To begin reviewing the tools available for TIN modeling, we will first import a set of vertices from a text file. These vertices are simply a set of xyz points entered into a TIN file. The TIN file format is described in the GMS File Format document. To import the vertices: 1. If necessary, switch to the TIN module. 2. Select the Open command from the File menu. 3. At the bottom of the Open dialog, select the *.tin filter. 4. In the Read File dialog, locate and open the directory entitled tutorial\tins. 5. Select the file entitled verts.tin. 6. Select the Open button. A set of points should appear on the screen.

19 Surface Modeling With TINs Triangulating To construct a TIN, we must triangulate the set of vertices we have imported. To triangulate the points: Select the Triangulate command from the Build TIN menu. The vertices should now be connected with edges forming a network of triangles. The triangulation is performed automatically using the Delauney criterion. The Delauney criterion ensures that the triangles are as "equiangular" as possible. In other words, wherever possible, long thin triangles are avoided. A more complete description of the triangulation algorithm can be found in Chapter 4 of the GMS Reference Manual. 2.5 Contouring Now that the TIN is constructed, we can use it to generate a contour plot of the TIN elevations. 1. Select the Display Options macro. 2. Turn on the Contours and TIN Boundary options and turn off the Triangles and Vertices options. 3. Select the OK button. The contours are generated by assuming that the TIN defines a surface that varies linearly across the face of each triangle. 2.6 Shading Another way to visualize a TIN is to shade the TIN. 1. Select the Display Options macro. 2. Turn off the Contours and TIN Boundary options and turn on the Triangles option. 3. Select the OK button. 4. Select the Oblique View macro. 5. Select the Shade macro.

20 2-4 GMS Tutorials 2.7 Editing TINs As TINs are used in the construction of solids and meshes, it is usually necessary to edit a TIN once it has been created. In many cases, TINs are constructed from a sparse set of points and it is necessary to "fill in the gaps" between the vertices and "sculpt" the TIN using the editing tools to ensure that the TIN is a reasonable representation of the surface being modeled. A variety of tools are provided in GMS for editing TINs. Before reviewing these tools, we will reset some of the display options. 1. Select the Display Options macro. 2. Turn on the Vertices and Contours options. 3. Select the Options button to the right of the Contours option. 4. In the section titled Contour Interval, select the Specified Interval option and change the interval to Select the OK button to exit the Contour Options dialog. 6. Select the Close button to exit the TIN Display Options dialog. 2.8 Dragging Vertices One of the simplest ways to edit a TIN is to drag the vertices with the cursor. This can be accomplished with the Select Vertices tool. 1. Choose the Select Vertices tool from the Tool Palette. 2. Select the Plan View macro. 3. Choose one of the vertices in the interior of the TIN and drag it to a new location. Notice that as you move the vertex, the contours of the TIN are instantaneously updated to give you visual feedback on the changes that you are making. You may have also noticed that you are not allowed to drag an interior vertex beyond the boundaries of the adjacent triangles. This prevents the triangles from becoming inverted.

21 Surface Modeling With TINs Dragging in Oblique View When dragging in plan view, the vertex is constrained to move in the xy plane. To change the z coordinate, we must drag the vertices in oblique view (or front or side view). 1. Select the Oblique View macro. 2. Select one of the vertices and drag the vertex up and down. Notice that as you drag the vertex in oblique view, you are constrained to move the vertex along the z axis Using the Edit Window In many cases, dragging vertices with the mouse is not adequately precise. It is often necessary to change the vertex coordinates to a specific value. This type of editing can be accomplished with the input fields at the top of the GMS window. Choose one of the vertices in the TIN and select it by clicking on it with the cursor. Notice that as the vertex is selected, the coordinates of the vertex are displayed in the fields at the top of the window. The edit fields can be used to change the x, y, or z coordinates of the selected vertex. 1. Move the cursor to the z coordinate field and add a value of 5.0 to the current z value of the vertex. 2. Hit the Return or Tab key. Again, as the vertex coordinates change, the triangle edges and contours of the surface are immediately updated Locking Vertices In many cases, some of the vertices defining a TIN come from actual measured data such as a borehole log and can be considered "hard" data. In other cases, vertices are added manually and represent "soft" data used simply to fill in gaps. When editing a TIN, it is useful to distinguish between these two types of vertices so that a vertex corresponding to an actual measurement is not accidentally edited. This can be accomplished by "locking" and "unlocking" vertices.

22 2-6 GMS Tutorials 1. Select several vertices by dragging a box around the vertices or by clicking on individual vertices while holding down the Shift key. 2. Select the Lock/Unlock Vertices command from the Modify TIN menu. Notice that the color of the vertices changes when they are locked. Once a set of vertices is locked, the coordinates of the vertices cannot be changed. 1. Click once outside the TIN to unselect the vertices. 2. Select one of the vertices that you just locked. 3. Attempt to edit the vertex by dragging or by entering new coordinates in the Edit Window. Locked vertices can be unlocked by selecting the vertices and selecting the Lock/Unlock Vertices command from the Modify TIN menu Adding Vertices As mentioned above, when working with TINs it is often necessary to edit a TIN by adding supplemental vertices to the TIN to provide more resolution or detail in an area of interest. Vertices can be added to a TIN in GMS simply by pointing and clicking. 1. Select the Plan View macro. 2. Select the Create Vertex tool. 3. Place the cursor in the interior of one of the triangles in the TIN and create a vertex by clicking the mouse button. A dialog appears prompting for the z value of the new vertex. The default value is computed using a linear interpolation of the surrounding vertices. Select the OK button to accept the default value. Notice that the vertex was automatically incorporated into the TIN topology. In addition, the vertex is selected and can be edited using the edit fields in the Edit Window Deleting Vertices It is also frequently necessary to delete vertices. To delete the vertex you just created:

23 Surface Modeling With TINs Select the Delete command from the Edit menu. 2. Select OK to confirm the deletion. Notice that all of the triangles connected to the vertex were deleted. By default, this is what happens when a vertex is deleted. The resulting void can be filled with triangles by using the Create Triangle tool to manually create triangles. However, another option is available for deletion that causes the region surrounding a deleted vertex to be automatically retriangulated. 1. Select the Vertex Options command from the Modify TIN menu. 2. Turn on the option entitled Retriangulate after deleting. 3. Select the OK button. 4. Choose the Select Vertices tool. 5. Select one the vertices in the interior of the TIN. 6. Select the Delete command from the Edit menu. 7. Select OK to confirm the deletion. Notice that the triangles next to the deleted vertex are deleted but the resulting void is retriangulated Smoothing a TIN As mentioned above, a TIN represents a piecewise linear surface. If the vertices defining the TIN are sparse, the linear surface defined by the triangles may appear excessively irregular. A TIN can be smoothed in GMS by copying the TIN vertices to a scatter point set, subdividing the TIN into a denser set of triangles, and interpolating the elevations to the new vertices in the TIN. The resulting TIN is still piecewise linear but it appears much smoother since the triangles are smaller Deleting the TIN We will now go through an example of TIN smoothing, but first we will read in a different TIN since we have made several changes to this TIN. 1. Select the Delete All command from the Edit menu. 2. Select OK to confirm the deletion.

24 2-8 GMS Tutorials 3. Select the Open command from the File menu. 4. Select No at the prompt about saving the project. 5. In the Open dialog, select the *.tin filter. 6. Select the file entitled "sparse.tin". 7. Click on the Open button Copying the Vertices The first step in smoothing the TIN is to copy the vertices of the TIN to a scatter point set. This will allow us to use the scatter point set later to interpolate the z values of the original vertices to the new vertices created while subdividing the TIN. 1. Select the TIN -> Scatter Points command in the Build TIN menu. 2. Select the OK button to accept the default name of the new scatter point set. 3. Select the No button to indicate that you do not want to delete the existing TIN Subdividing the TIN The next step is to increase the resolution of the TIN by uniformly subdividing the TIN. 1. Select the Uniformly Subdivide TIN command from the Modify TIN menu. 2. Move the scroll bar to select a subdivision factor of Select the OK button Interpolating the Elevations Notice that the contours of the TIN have not changed. There are more triangles in the TIN but they still define essentially the same surface. To smooth the TIN we must use one of the interpolation schemes and interpolate from the original vertices of the TIN to the new vertices created during the subdivision process. 1. Switch to the 2D Scatter Point module.

25 Surface Modeling With TINs Select the to Active TIN command from the Interpolation menu (we will use the default interpolation method). 3. Enter a name of "new_elev" for the new data set. 4. Turn on the Map elevations option. This ensures that the data set created on the TIN will be used to define the elevations of the TIN vertices. 5. Select the OK button. The contours on the TIN now appear smoother. To better view the variation in the surface: Select the Oblique View macro Deleting the Scatter Point Set The TIN smoothing process is now completed. Since we no longer need the scatter point set, we will delete it. 1. Select the Delete All command from the Edit menu. 2. Select the OK button to confirm the deletion Reading Another TIN In GMS, several TINs can be modeled at once. For example, we will now read in another TIN without first deleting the existing TIN. 1. Switch to the TINs module. 2. Select the Open command from the File menu. 3. Select No at the prompt about saving the project. 4. In the Open dialog, select the *.tin filter. 5. Select the file entitled "surface.tin". 6. Click on the Open button. You should now see two TINs displayed at once.

26 2-10 GMS Tutorials 2.16 Changing the Active TIN Whenever multiple TINs are being modeled, one of the TINs is designated as the active TIN. Only the active TIN can be edited. A TIN can be designated as the active TIN using the combo box at the top of the GMS window. 1. Choose the Select TINs tool. 2. In the combo box titled "TIN", select the "sparse" item. Notice that triangular shaped icons appear at the center of each TIN. A TIN is selected by selecting the TIN icon. The active TIN has a letter "A" displayed in the center of the icon. A TIN can also be designated as the active TIN by double clicking on the TIN icon. For example: Double click on the TIN icon entitled "surface". The letter "A" is now displayed in the icon for the TIN we just read from a file. This TIN can now be edited Hiding and Showing TINs When multiple TINs are in memory, it is sometimes useful to hide some of the TINs temporarily. This makes the display less cluttered and makes it easier to edit or visualize an individual TIN. For example: 1. Select the TIN entitled "sparse" by clicking once on the TIN icon. 2. Select the Hide macro from the Tool Palette Deleting the TINs Since we are now finished with the TINs, we will delete them. 1. Select the New command from the File menu. 2. Select the No button to confirm the deletion Conclusion This concludes the Surface Modeling With TINs tutorial. Now that you have finished this tutorial and understand the basics of TIN modeling, you are

27 Surface Modeling With TINs 2-11 prepared to proceed to the tutorial entitled Stratigraphy Modeling with Solids (Chapter 3). If you were originally running in normal mode and switched to demo mode to complete this tutorial, you can switch back to normal mode as follows: 1. Select the Normal Mode command from the File menu. 2. Select the OK button at the prompt. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

28

29 3 Stratigraphy Modeling With Solids CHAPTER 3 Stratigraphy Modeling With Solids The Solid module of GMS is used to construct three-dimensional models of stratigraphy. Once such a model is created, cross sections can be cut anywhere on the model and hidden surface removal and shading can be used to generate highly realistic images of either the cross sections or the solids. Volumes of solids can also be computed. In this tutorial you will learn how to construct a set of solid models representing soil stratigraphy using borehole data as input. Since TINs are used in the construction of solids, you should first complete the tutorial entitled Surface Modeling with TINs (Chapter 2) before beginning this tutorial. It is also helpful if you read the introduction to the chapter describing the Solid module in the GMS Reference Manual. This will give you a basic understanding of the approach used to construct solid models. 3.1 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state. 3.2 Required Modules/Interfaces This tutorial can be completed in either demo mode or normal model. If you are already in demo mode, you may continue with the tutorial. If you are in normal mode, you will need to ensure that the necessary components have

30 3-2 GMS Tutorials been licensed. This tutorial utilizes the following components of the GMS interface: The TIN module The Borehole module The Solid module The Map module You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If each of these items is enabled, you can proceed to complete the tutorial in normal mode. If not, you will need to switch to demo mode before continuing. To switch to demo mode: 1. Select the Demo Mode command from the File menu. 2. Select OK at the prompts. 3.3 Constructing the Solid Models Constructing a set of solid models of soil stratigraphy in GMS is a three step process. In the first step, a set of boreholes is input. In the next step, a set of surfaces (TINs) is constructed through contacts on the boreholes which are selected by the user. These surfaces represent the interfaces between adjacent soil layers. In the third step, the surfaces are used to construct solid models of the soil layers. 3.4 Reading Borehole Data The first step in the construction of the solid models is to import a set of borehole logs. Borehole data can be entered one of two ways. The data can be entered into a text file in the GMS borehole file format described in the GMS Reference Manual. Alternately, the boreholes can be entered one at a time using the Borehole Editor command in the Boreholes menu. In the interest of time, we will use the first approach and import a set of boreholes from a previously prepared borehole file. The borehole data in this file were obtained from an actual site investigation. To read in the file:

31 Stratigraphy Modeling With Solids Switch to the Borehole module. 2. Select the Open command from the File menu. 3. Locate and open the directory entitled tutorial\solids. 4. Select the file entitled holes.gpr. 5. Click on the Open button. You should now see a 3D view of the borehole logs. Each of the colors represents a different type of soil. The green soil is a clean sand, the red soil is a silty sand, and the blue soil is a silty clayey fine sand. For the remainder of this tutorial, the soils will be referred to by their colors for simplicity. 3.5 Changing the Z Scale In some cases, it is useful to magnify the display in the z dimension so that the variation in the stratigraphy depicted by the borehole logs is more apparent. To change the z scale: 1. Select the Z Magnification command from the View menu. 2. Enter a value of Select the OK button. The holes should now appear "stretched" in the vertical direction. 3.6 Displaying the Hole Names To help distinguish between the holes on the screen throughout the remainder of the tutorial, the names of the holes will be posted on the holes. 1. Select the Display Options macro. 2. Turn on the Hole Names option. 3. Select the OK button. The names of the holes should appear at the tops of the holes. These names were defined in the borehole file.

32 3-4 GMS Tutorials 3.7 Creating an Extrapolation Polygon The next step in the construction of the stratigraphy model is to create a set of TINs that represent the interfaces between the soil layers depicted in the borehole data. However, before constructing the TINs, we must first define an extrapolation polygon. The extrapolation polygon defines the boundary or the limits of the stratigraphy model. In many cases, the polygon corresponds to a property boundary Setting Up the View The extrapolation polygon will just enclose the boreholes. The polygon will be entered in plan view. Select the Plan View macro. To allow plenty of screen space to enter the polygon we will increase the viewing area (zoom out). 1. Select the Zoom tool. 2. While holding down the Shift key, click somewhere in the center of the boreholes Turning on the Drawing Grid We will be entering the extrapolation polygon interactively using the mouse. To help guide the placement of the polygon, we will temporarily turn on a drawing grid. 1. Select the Drawing Grid Options command from the Display menu. 2. Set the Spacing to Turn on the Snap to grid option. 4. Turn on the Display grid lines option. 5. Set the Grid line spacing increment to Select the OK button. You should see a grid appear on the screen. Notice that as you move the cursor across the Graphics Window, the coordinates that appear in the Edit Window at the bottom of the screen move in increments of 50.

33 Stratigraphy Modeling With Solids Defining the Boundary Arc We are now ready to enter the extrapolation polygon. The extrapolation polygon is entered using the feature object tools in the Map module. First, we will create a single arc defining a closed loop around the site. 1. Switch to the Map module. 2. Select the Create Arc tool. 3. Create a single arc by clicking on the points shown in Figure 3.1 (clockwise or counter-clockwise - it does not matter). To ensure you are placing the points in the proper location, note the cursor coordinates displayed on the left side of the Edit Window. Begin with the point (50, 700). To close the polygon, double click on the point you started with. (50, 700) (250, 700) 2G 5G 7G 6G 1G (600, 400) 4G 3G 8G (50, 50) (600, 50) Figure 3.1 The Coordinates of the Points Defining the Extrapolation Polygon Creating the Polygon Now that we have created the arc, we must use the arc to build a polygon. 1. Select the Build Polygons command from the Feature Objects menu. 2. Select OK at the prompt to use all arcs.

34 3-6 GMS Tutorials The Build Polygons command traverses the set of currently defined arcs and makes polygons out of all of the closed loops found. This is trivial in this case since there is only one arc and one closed loop Turning off the Drawing Grid Now that the polygon is entered, you can turn off the drawing grid. 1. Select the Drawing Grid Options command from the Display menu. 2. Turn off the Snap to grid option. 3. Turn off the Display grid lines option. 4. Select the OK button. 5. Select the Oblique View macro. 3.8 Constructing the Ground Surface TIN You are now ready to construct a TIN using the borehole logs. We will begin by constructing a TIN representing the ground surface. This TIN will pass through the top of each of the boreholes Selecting the Contacts Before constructing the TIN, you must first select the contacts (locations on the boreholes) that will be used to create the TIN. 1. Switch to the Borehole module. 2. Choose the Select Contacts tool. 3. While holding the Shift key, click on the top of each of the holes Creating the TIN Now that you have selected the points on the boreholes where the TIN is to pass through, you can construct the TIN by triangulating the points. 1. Select the Contacts -> TIN command from the Boreholes menu. 2. Select the Auto-extrapolate only option.

35 Stratigraphy Modeling With Solids Select the OK button. 4. Enter "topblue1" for the name of the TIN. 5. Select the OK button. A blue TIN should appear. Note that the TIN passes through the borehole contacts that were selected and it also extends out to the extrapolation polygon. This TIN could now be edited, if desired, using the TIN editing tools described in the previous tutorial to smooth or reshape the TIN. For the purposes of this tutorial, the TIN is adequate as is and will not be edited Hiding the TIN Before continuing, it is useful to hide the TIN so that it will not be cluttering the display while the other TINs are being constructed. To hide the TIN: 1. Switch to the TIN module. 2. Choose the Select TINs tool. 3. Select the TIN you just created by clicking on its icon. 4. Select the Hide macro. 5. Switch back to the Borehole module. 3.9 Constructing the Green Seam TIN Next, we will construct the TIN representing the top of the green seam that cuts through the side. To select the contacts: 1. Choose the Select Contacts tool. 2. Select the blue/green contact on hole 3G Automatically Selecting Contacts We could now select the remaining contacts one at a time with the Shift key down as we did last time. However, this time we will use the Auto Select command to select the remaining holes. The Auto Select command is used to select a set of contacts that match a previously selected contact. 1. Select the Auto Select command from the Boreholes menu.

36 3-8 GMS Tutorials 2. Select the OK button Creating the TIN All of the contacts at the top of the green soil should now be selected. To construct the TIN: 1. Select the Contacts -> TIN command from the Borehole menu. 2. Select the Auto-extrapolate with trimming to selected boreholes option. 3. Select the OK button. 4. Enter "topgreen" for the name of the TIN. 5. Select the OK button. A green TIN should appear. Note that once again the TIN is automatically extended to the extrapolation polygon and in addition, the TIN is automatically extended to a point halfway between the holes that were selected and the holes that were not selected. Of course, this boundary could be edited, but it provides a reasonable initial estimate of the extent of the surface defined by the selected contacts. For the purposes of this tutorial, we will accept the default surface Hiding the TIN To hide the TIN: 1. Switch to the TIN module. 2. Choose the Select TINs tool. 3. Select the TIN you just created by clicking on its icon. 4. Select the Hide macro. 5. Switch back to the Borehole module Constructing the Red Soil TIN Next, we will construct the TIN representing the top of the red soil unit at the lower part of the stratigraphy.

37 Stratigraphy Modeling With Solids Constructing the TIN To construct the TIN: 1. Choose the Select Contacts tool. 2. Select the blue/red contact on hole 4G. 3. Select the Auto Select command from the Boreholes menu. 4. Turn off the Match material above option. 5. Select the OK button. 6. Select the Contacts -> TIN command from the Boreholes menu. 7. Select the Auto-extrapolate only option. 8. Select the OK button. 9. Enter "topred" for the name of the TIN. 10. Select the OK button Hiding the TIN To hide the TIN: 1. Switch to the TIN module. 2. Choose the Select TINs tool. 3. Select the TIN you just created by clicking on its icon. 4. Select the Hide macro. 5. Switch back to the Borehole module Constructing the Blue Seam TINs Most of the boreholes show a thin region of blue soil near the bottom of the holes. We will model this region as a blue seam which cuts diagonally through the site. This seam will lie entirely within the red soil. To model the seam, we will need to construct two TINs: one at the top of the seam and one at the bottom.

38 3-10 GMS Tutorials Constructing the Top TIN To construct the TIN at the top of the seam: 1. Choose the Select Contacts tool. 2. Select the red/blue contact on hole 8G (see Figure 3.2). 3. Select the Auto Select command from the Boreholes menu. 4. Select the OK button. 5. Select the Contacts -> TIN command from the Boreholes menu. 6. Select the Auto-extrapolate with trimming to selected boreholes option. 7. Select the OK button. 8. Enter "topblue2" for the name of the TIN. 9. Select the OK button. 8G Select this contact Figure 3.2 Contact on Hole 8G to be Selected Constructing the Bottom TIN To construct the TIN at the bottom of the seam.

39 Stratigraphy Modeling With Solids Since the Auto Select command will not work in this case, hold down the Shift key and select the following contacts (see Figure 3.3): the lower blue/red contact on hole 8G. the bottom of hole 6G, the blue/red contact on hole 7G, the lower blue/red contact on hole 5G, and the bottom of hole 2G. 2. Select the Contacts -> TIN command from the Borehole menu. 3. Select the Auto-extrapolate with trimming to selected boreholes option. 4. Select the OK button. 5. Enter "botblue2" for the name of the TIN. 6. Select the OK button. 2G 5G 7G 4G 6G 1G 3G 8G Z Y X Figure 3.3 Contacts to be Selected.

40 3-12 GMS Tutorials Hiding the TINs To hide the TINs: 1. Switch to the TIN module. 2. Choose the Select TINs tool. 3. While holding down the Shift key, select the two TINs you just created. 4. Select the Hide macro Constructing the Red Solid Now that all of the TINs are constructed, we are ready to construct the solid models from the TINs. To begin, we will construct the solid representing the red soil. This solid will be constructed by extruding the boundary of the red TIN down to a horizontal plane below the boreholes Creating the Solid To create the solid: 1. Select the TIN entitled "topred". 2. Select the Extrude TIN -> Solid command from the Build TIN menu. 3. Enter "red" for the name of the solid. 4. Enter for the Elevation. 5. Select the OK button Shading the Solid A red solid should appear on the screen. The shape of the solid can be better illustrated by generating a shaded image. Select the Shade macro. To revert to wireframe view: Select the Refresh macro.

41 Stratigraphy Modeling With Solids Constructing the Blue Seam Next, we will construct the lower blue seam. This solid can be constructed simply by filling between the two TINs defining the top and the bottom of the seam. When this method is used, it is important that the top TIN is first selected followed by the bottom TIN. 1. Select the TIN entitled "topblue2". NOTE: In some cases, the TIN icons are grouped together and it is difficult to be sure your are selecting the proper TIN. In such cases, it is often helpful to select the Select from List command in the Edit menu. This command allows you to select a TIN by choosing the name of the TIN from the list of currently defined TINs. 2. While holding the Shift key, select the TIN entitled "botblue2". 3. Select the Fill Between TINs -> Solid command from the Build TIN menu. 4. Enter "blue2" for the name of the solid. 5. Select the OK button Subtracting the Blue Seam At this point, the blue seam and the red solid occupy the same space. To create an accurate stratigraphy model, we must make a hole in the red solid at the location of the blue seam. This can be accomplished by "subtracting" the blue seam from the red solid using a set operation. 1. Switch to the Solid module. 2. Choose the Select Solids tool. 3. Select the solid entitled "red". 4. While holding down the Shift key, select the solid entitled "blue2". 5. Select the Set Operations command from the Solids menu. 6. In the section entitled Operand #1, turn on the Delete option. This will delete the old version of the red solid once the set operation is completed since we won t need it anymore.

42 3-14 GMS Tutorials 7. Select the minus operation. 8. Enter "red" for the name of the new solid resulting from the set operation. 9. Select the OK button. The red solid now has a hole in it at the location of the blue seam. To confirm: Select the Shade macro. To revert to wireframe view: Select the Refresh macro Constructing the Green Solid Next, we will construct the solid representing the green seam. This solid will be created by filling between the green TIN and the red TIN. 1. Switch to the TIN module. 2. Select the Select TINs tool. 3. Select the TIN entitled "topgreen". 4. While holding the Shift key, select the TIN entitled "topred". 5. Select the Fill Between TINs -> Solid command from the Build TIN menu. 6. Enter "green" for the name of the solid. 7. Select the OK button Constructing the Top Blue Solid Finally, we will construct the solid representing the top blue soil layer. This solid is bounded below by both the green solid and the red solid. However, it can still be constructed using the Fill Between TINs -> Solid command. The solid is constructed by filling from the blue TIN down to the red or green TIN, whichever is higher.

43 Stratigraphy Modeling With Solids Select the TIN entitled "topblue1". 2. While holding the Shift key, select the TIN entitled "topgreen". 3. While holding the Shift key, select the TIN entitled "topred". 4. Select the Fill Between TINs -> Solid command from the Build TIN menu. 5. Enter "blue1" for the name of the solid. 6. Select the OK button Viewing the Solids At this point, all of the solids are constructed and the stratigraphy model is complete. To view the model in shaded mode: Select the Shade macro Cross Sections Another useful way to visualize a stratigraphy model is to construct cross sections through the model Creating the Cross Sections To construct a set of cross sections: 1. Switch to the Solid module. 2. Select the Create Cross Section tool. 3. Select the Plan View macro. 4. Cut a cross section through the solids by clicking on one side of the solids, moving the cursor to the other side of the solids, and doubleclicking. Cut the solid through the line A-A as shown in Figure 3.4. Repeat this process to create cross sections at the lines B-B, C-C, D- D, and E-E.

44 3-16 GMS Tutorials D A 2G A E 7G B 5G 6G 1G B 4G 3G 8G C C D E Figure 3.4 Location of Cross Sections Hiding the Solids Before viewing the cross sections we need to select the solids and make them invisible. 1. Select the Select Solids tool from the Tool Palette. 2. Choose the Select All command from the Edit menu. 3. Select the Hide macro from the Tool Palette. 4. Select the Oblique View macro from the Tool Palette Deleting the Boreholes Since we no longer need the boreholes, we can remove them from the display by simply deleting them. 1. Switch to the Boreholes module. 2. Select the Delete All command from the Edit menu. 3. Select OK to confirm the deletion.

45 Stratigraphy Modeling With Solids Deleting the Polygon We will also delete the polygon. 1. Switch to the Map module. 2. Select the Delete All command from the Edit menu. 3. Select OK to confirm the deletion Shading the Cross Sections Once again, the cross sections are displayed as a wire frame image by default. We can shade the cross sections the same way we shaded the solids. Select the Shade macro from the Tool Palette. You may wish to use the Rotate tool to rotate the cross sections to a better viewing position and shade the solids again Layer Boundaries Notice that the boundaries of the green seam and the blue seam have an abrupt vertical edge rather than a gradually narrowing pinchout boundary which would seem more natural. A sharp pinchout at the boundary can be achieved by altering the coordinates of the TIN vertices prior to constructing the solids using the TIN editing tools described in the previous tutorial Deleting the Solids and TINs The solids and TINs can be deleted using the New command. The New command deletes all data in all modules. 1. Select the New command in the File menu. 2. Select the No button to confirm Conclusion This concludes the Stratigraphy Modeling with Solids tutorial. If you were originally running in normal mode and switched to demo mode to complete this tutorial, you can switch back to normal mode as follows:

46 3-18 GMS Tutorials 1. Select the Normal Mode command from the File menu. 2. Select the OK button at the prompt. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

47 4 2D Geostatistics CHAPTER 4 2D Geostatistics Two-dimensional geostatistics (interpolation) can be performed in GMS using the 2D Scatter Point module. The module is used to interpolate from sets of 2D scatter points to any of the other object types (meshes, grids, TINs). Several interpolation schemes are supported, including kriging. Geostatistics are useful for setting up input data for analysis codes or for site characterization. The tools for manipulating scatter point sets and the interpolation schemes supported in GMS are described in this tutorial. The interpolation schemes presented in this tutorial will be easier to understand if you have read Chapter 9 of the GMS Reference Manual. This tutorial should be completed before attempting the Three-Dimensional Geostatistics tutorial. 4.1 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state. 4.2 Required Modules/Interfaces This tutorial can be completed in either demo mode or normal model. If you are already in demo mode, you may continue with the tutorial. If you are in normal mode, you will need to ensure that the necessary components have

48 4-2 GMS Tutorials been licensed. This tutorial utilizes the following components of the GMS interface: The 2D Scatter Point module The 2D Grid module You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If each of these items is enabled, you can proceed to complete the tutorial in normal mode. If not, you will need to switch to demo mode before continuing. To switch to demo mode: 1. Select the Demo Mode command from the File menu. 2. Select OK at the prompts. 4.3 Importing a Scatter Point Set Interpolation in GMS is performed using scatter points. A set of 2D scatter points is defined by a set of xy coordinates. A group of scatter points is called a scatter point set. Each scatter point set has a list of scalar data sets. Each data set represents a set of values that can be interpolated to a TIN, mesh, or grid. To begin the tutorial, we will import a scatter point set. The scatter point set has been entered into a previously prepared text file using the Tabular Scatter Point File format described in the GMS File Formats document. This format is designed for importing scatter point sets only. GMS saves scatter point sets using a different format. The format uses a simple tabular approach that can be easily prepared using a spreadsheet or text editor. The file we will import was generated as an Excel spreadsheet and exported from Excel as tab delimited text. To read the scatter point file: 1. Switch to the 2D Scatter Point module. 2. Select the Import command from the File menu. 3. At the bottom of the Open dialog, change the filter to *.sp2. 4. Locate and open the directory entitled tutorial\geos2d. 5. Select the file entitled plumedat.sp2.

49 Two-Dimensional Geostatistics Click on the Open button. A set of points should appear on the screen. These points represent locations where the concentration of a contaminant has been estimated using a soil gas survey. Our goal is to generate a map of the contaminant plume. 4.4 Changing the Display Options You can change the appearance of the scatter points using the Display Options dialog: 1. Select the Display Options macro. 2. Turn on the Data colors option 3. Select the button to the left of the Scatter point symbols toggle. 4. Choose one of the triangle shaped symbols. 5. Select the OK button to exit the Symbol Picker dialog. 6. Select the OK button to exit the Display Options dialog. Each of the points should now be displayed with a colored triangle. The color of the symbol represents the relative concentration of the contaminant at the point. When displaying colored symbols, it is useful to also display a color legend. 1. Select the Color Ramp Options command from the Data menu. 2. Turn on the Show Color Legend option. 3. Select the OK button. Notice that the concentrations vary from zero to about Creating a Bounding Grid The goal of this tutorial is to generate a series of contour plots illustrating the plume. To do this we will first create a grid that bounds the scatter point set and then we will interpolate the concentrations from the scatter points to the grid nodes. The grid will then be contoured. To create the grid:

50 4-4 GMS Tutorials 1. Select Bounding Grid from the Scatter Points menu. Notice that the x and y dimensions of the grid are already defined. The default values shown in the dialog cause the grid to extend beyond the scatter points by 10% on each side. 2. Enter 60 for the number of cells in the x direction 3. Enter 40 for the number of cells in the y direction. 4. Select the OK button. 5. Select the OK button to accept the default z value. A grid should appear on the screen that just encompasses the scatter point set. 4.6 Selecting an Interpolation Scheme The next step is to select an interpolation scheme. Several interpolation schemes are supported in GMS because there is no one interpolation scheme that is superior in all situations. Typically, the best approach is to try several schemes and then determine which scheme is giving the most reasonable results. GMS has been structured in such a way that several different schemes can be tested quickly and easily. 4.7 Linear Interpolation First we will try simple linear interpolation. 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Linear option. 3. Select the OK button. To interpolate to the grid: 1. Select the to 2D Grid command from the Interpolation menu. 2. Enter "linear" for the name of the new data set. 3. Select the OK button.

51 Two-Dimensional Geostatistics Contouring the Grid The concentrations have been interpolated to the grid but we must first set the appropriate display options before we can see the resulting contours. 1. Switch to the 2D Grid module. 2. Select the Display Options macro. 3. Turn on the Contours and Fringes options. 4. Turn off the Nodes option. 5. Select the OK button. A set of contours should now be displayed. 4.9 Mapping Elevations It is often useful to display the grid in oblique view. Select the Oblique View macro. Note that the grid is flat. When we created the grid we assigned a z value of 0.0 to all of the grid nodes. To make the variation in concentrations easier to visualize, we can use the Map Elevations command to load the concentration data set values into the z coordinates of the grid nodes. 1. Select the Map Elevations command from the Data menu. 2. Select the data set entitled "linear". 3. Choose the OK button Shading the Grid Color shading and hidden surface removal can be applied to provide an even more effective display of the grid. Select the Shade macro. Notice that the nodes in the outer part of the grid still all have a concentration value equal to zero. When linear interpolation is performed, the scatter points are triangulated to form a temporary TIN. A plane equation is computed for

52 4-6 GMS Tutorials each triangle in the TIN and the coefficients of the plane equation are used to interpolate to points inside the triangle. Therefore, linear interpolation cannot be performed for grid nodes outside the convex hull of the TIN (the boundary of the TIN). As a result, these nodes are assigned a value of zero. However, for this application, a value of zero is appropriate since the concentrations of the scatter points on the perimeter of the scatter point set are zero Clough-Tocher Interpolation Next, we will try Clough-Tocher interpolation. 1. Switch to the 2D Scatter Point module. 2. Select the Interp. Options command from the Interpolation menu. 3. Select the Clough-Tocher option. 4. Select the OK button. To interpolate to the grid: 1. Select the to 2D Grid command from the Interpolation menu. 2. Enter "ct" for the name of the new data set. 3. Turn on the Map Elevations toggle. Note: This will cause the interpolated concentrations to be automatically mapped to the z coordinates of the nodes as the data set is interpolated. 4. Select the OK button. 5. Select the Shade macro. Once again, interpolation was only performed within the convex hull of the scatter point set. As with linear interpolation, the first step in Clough-Tocher interpolation is to triangulate the scatter point set to form a temporary TIN. However, rather than performing a linear interpolation of each triangle, a cubic surface patch is fitted over each triangle and the cubic patches are used in the interpolation.

53 Two-Dimensional Geostatistics Simple IDW Interpolation The next scheme we will try is a simple form of inverse distance weighted (IDW) interpolation. 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Inverse distance weighted option. 3. Select the Options button to the right of the Inverse distance weighted option. 4. In the Nodal function section at the top of the dialog, select the Constant option. 5. In the section entitled Computation of interpolation weights, select the Use all points option. 6. Select the OK button to exit the 2D IDW Interpolation Options dialog. 7. Select the Close button to exit the 2D Interpolation Options dialog. To interpolate to the grid: 1. Select the to 2D Grid command from the Interpolation menu. 2. Enter "idw_const" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro. The IDW scheme is a simple moving weighted averages scheme. To interpolate a value at a point, a weighted average of the nearby scatter points is used. The weights are an inverse function of distance. The closer a scatter point is to the interpolation point, the greater the weight given to the scatter point IDW Interpolation With Gradient Planes One of the problems with simple IDW interpolation is that the interpolated data set always tends toward the mean of the data set in the voids between scatter points. As a result, local minima or maxima in the voids in the scatter point set are not properly inferred. To overcome this problem, a "nodal function" can be computed at each scatter point. A nodal function is a plane or quadratic function that is forced to pass through the scatter point and approximate the nearby scatter points in a least squares sense. When the

54 4-8 GMS Tutorials interpolation is performed, rather than computing an average of the data set values at the scatter point locations, an average is computed of the nodal functions of the nearby scatter point evaluated at the interpolation point. This approach allows local trends to be inferred and often results in a more accurate interpolation. The next scheme we will try is IDW interpolation with planar nodal functions. 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Options button to the right of the Inverse distance weighted option. 3. In the Nodal function section at the top of the dialog, select the Gradient plane option. 4. Select the OK button to exit the 2D IDW Interpolation Options dialog. 5. Select the Close button to exit the 2D Interpolation Options dialog. To interpolate to the grid: 1. Select the to 2D Grid command from the Interpolation menu. 2. Enter "idw_planar" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro IDW Interpolation With Quadratic Nodal Functions The nodal functions used in IDW interpolation can also be quadratic functions which are constrained to pass through the scatter point and approximate the neighboring scatter points in a least squares fashion. The averaging or blending of the quadratic functions during the interpolation stage often results in a very smooth surface. 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Options button to the right of the Inverse distance weighted option. 3. In the Nodal function section at the top of the dialog, select the Quadratic option. 4. Select the OK button to exit the 2D IDW Interpolation Options dialog.

55 Two-Dimensional Geostatistics Select the Close button to exit the 2D Interpolation Options dialog. To interpolate to the grid: 1. Select the to 2D Grid command from the Interpolation menu. 2. Enter "idw_quad" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro Truncation Notice that the minimum value listed in the color legend is Of course, this is impossible since there is no such thing as a negative concentration. By inferring trends, the nodal functions can sometimes project the plume values beyond zero and into the negative range. This type of error can be easily fixed using truncation. 1. Select the Interp. Options command from the Interpolation menu. 2. Turn on the Truncate values option. 3. Select the Truncate to specified range option. 4. Enter 0.0 for the min value and enter for the max value. We don t want the concentrations to go below zero but we will allow the interpolation scheme to infer a maximum concentration greater that the maximum measured value. 5. Select the OK button. To interpolate to the grid: 1. Select the to 2D Grid command from the Interpolation menu. 2. Enter "idw_quad_trunc" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro. Notice that the concentrations are now mostly zero around the perimeter of the map.

56 4-10 GMS Tutorials 4.16 Natural Neighbor Interpolation Next, we will test the natural neighbor interpolation. Natural neighbor is similar to IDW interpolation in that it is a moving weighted average approach. However, the technique used to compute the weights in natural neighbor interpolation is based on topological relationships rather than distance alone. This approach tends to provide good results even when the scatter points are clustered. 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Natural neighbor option. 3. Select the Options button to the right of the Natural neighbor option. As with IDW interpolation, we can use higher order nodal functions if desired. We will use the quadratic option. 1. Select the Quadratic option. 2. In the Bounding pseudo-points section, turn OFF the Extrapolate beyond convex hull option. Natural neighbor interpolation triangulates the scatter points as part of the interpolation process. The boundary of the resulting TIN corresponds to the convex hull of the scatter points. Computing points outside this hull is considered to be extrapolation. If the values are not extrapolated, a zero value is assigned to the grid nodes outside the convex hull. Thus, turning off the Extrapolate beyond convex hull option is a simple way to ensure that the concentrations on the perimeter of the map are zero. 3. Select the OK button to exit the Natural Neighbor Options dialog. 4. Select the Close button to exit the 2D Interpolation Options dialog. To interpolate to the grid: 1. Select the to 2D Grid command from the Interpolation menu. 2. Enter "nn" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro.

57 Two-Dimensional Geostatistics Kriging The last interpolation scheme we will test is kriging. Kriging is based on the assumption that points that are near each other have a certain degree of spatial correlation, but points that are widely separated are statistically independent. Kriging is a set of linear regression routines that minimize estimation variance from a predefined covariance model. 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Kriging option. 3. Select the Options button to the right of the Kriging option Creating the Experimental Variogram There are a large number of options to be specified in the Kriging Options dialog. Fortunately, the defaults shown are adequate in most cases. However, a variogram must always be defined. 1. Select the Edit Variograms button. 2. Select the New button in the section entitled Experimental variogram editor in the upper right section of the Variogram Editor dialog. 3. Select the OK button to accept the defaults. A curve should appear in the upper left window of the Variogram Editor. This curve is called an experimental variogram. The experimental variogram is found by calculating the variance in data set values of each scatter point in the set with respect to each of the other points and plotting the variances versus distance between the points. As can be seen in the plot of the experimental variogram, the shape of the variogram indicates that at small separation distances, the variance is small. In other words, points that are close together have similar data values. With many data sets, after a certain level of separation, the variance in the data values becomes somewhat random and the variogram oscillates about a value corresponding to the average variance. However, with concentration data, many of the points have zero values and this tends to pull the experimental variogram back down Creating the Model Variogram Once the experimental variogram is computed, the next step is to define a model variogram. A model variogram is a simple mathematical function that models the trend in the experimental variogram. The model variogram is used in the kriging computations.

58 4-12 GMS Tutorials 1. Select the New button in the section entitled Nested structure specification in the lower right corner of the Variogram Editor. 2. In the section entitled Model functions on the left side of the dialog, select the Gaussian option. 3. In the section entitled Model parameters, enter a value of for the Contribution and a value of 63.0 for the Range. Select the Tab key after entering each value. At this point there should be a reasonable fit between the model and first part of the experimental variogram. The second part is difficult to fit in this case because of the zero values described above. 4. Select the OK button to exit the Variogram Editor. 5. Select the Close button to exit the Kriging Options dialog. 6. Select the Close button to exit the 2D Interpolation Options dialog Interpolating to the Grid To interpolate to the grid: 1. Select the to 2D Grid command from the Interpolation menu. 2. Enter "krig" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro Switching Data Sets Now that we have interpolated to the grid using several different interpolation schemes, we may wish to review the results by replotting some of the interpolated data sets. We can switch back to one of the previous data sets using the combo boxes at the top of the GMS window. 1. Switch to the 2D Grid module. 2. In the combo box titled Data Set, select the linear item. Notice that the contours of the grid have changed but the elevations still correspond to the previous data set (kriging). To change the elevations to the

59 Two-Dimensional Geostatistics 4-13 new data set we must select the Map Elevations command as explained earlier. However, in this case we will simply view the plot in plan view. Select the Plan View macro. We can display a color shaded plot in plan view by changing the contouring options. 1. Select the Display Options macro. 2. Turn off the Cells option and turn on the Grid boundary option. 3. Select the Options button to the right of the Contours option. 4. In the Contour method section in the lower left corner of the dialog, select the Color fill between contours option. 5. Select OK to exit the Contour Options dialog. 6. Select Close to exit the 2D Grid Display Options dialog Using the Data Calculator Occasionally, it is useful to use the Data Calculator to compare two data sets generated by interpolation. As an example, we will use the Data Calculator to compute the difference between the kriging and natural neighbor data sets. Select the Data Calculator command from the Data menu. The currently available data sets are listed in the top of the dialog. Each data set is assigned a letter. Data sets are referenced in the mathematical expression using the letters. The "krig" data set should be labeled "i" and the "nn" data set should be labeled "h". The next step is to enter an expression to compute the absolute value of the difference between the krig and nn data sets. 1. In the Expression field, enter "abs(h-i)". 2. In the Result field, enter "Difference". 3. Select the Compute button. Now that we have computed the difference between two data sets it is helpful to view some basic statistics related to the new data set.

60 4-14 GMS Tutorials Select the Data Set Info button. The resulting dialog displays basic statistics related to the active data set such as minimum, maximum, and mean data values. 1. Select the OK button to exit the Scalar Data Set Info dialog. 2. Select the Done button to exit the Data Calculator dialog. The contour plot now displayed represents the data set we just computed. Any new data set computed using the Data Calculator is automatically designated the active data set Deleting All Data To delete all of the data we have generated in this tutorial from memory: 1. Select the New command from the File menu. 2. Select No to confirm the deletion Conclusion This concludes the Two-Dimensional Geostatistics tutorial. If you were originally running in normal mode and switched to demo mode to complete this tutorial, you can switch back to normal mode as follows: 1. Select the Normal Mode command from the File menu. 2. Select the OK button at the prompt. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

61 5 3D Geostatistics CHAPTER 5 3D Geostatistics Three-dimensional geostatistics (interpolation) are performed in GMS using the 3D Scatter Point module. The module is used to interpolate from sets of 3D scatter points to 3D meshes and 3D grids. Several interpolation schemes are supported, including kriging. Interpolation is useful for defining initial conditions for 3D ground water models or for 3D site characterization. The tools for manipulating 3D scatter point sets and the interpolation schemes supported in GMS are described in this tutorial. Before attempting this tutorial you should have completed the Two-Dimensional Geostatistics tutorials. 5.1 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state. 5.2 Required Modules/Interfaces This tutorial can be completed in either demo mode or normal mode. If you are already in demo mode, you may continue with the tutorial. If you are in normal mode, you will need to ensure that the necessary components have been licensed. This tutorial utilizes the following components of the GMS interface: The 3D Scatter Point module

62 5-2 GMS Tutorials The 3D Grid module You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If each of these items is enabled, you can proceed to complete the tutorial in normal mode. If not, you will need to switch to demo mode before continuing. To switch to demo mode: 1. Select the Demo Mode command from the File menu. 2. Select OK at the prompts. 5.3 Importing a Scatter Point Set To begin the tutorial, we will import a 3D scatter point set. A 3D scatter point set is similar to a 2D scatter point set except that each point has a z coordinate in addition to xy coordinates. As with the 2D scatter point set, one or more scalar data sets can be associated with each scatter point set representing values such as contaminant concentration, porosity, hydraulic conductivity, etc. The 3D scatter point set we will import and use with this tutorial has previously been entered into a text file using the Tabular Scatter Point File format. To read the scatter point file: 1. Switch to the 3D Scatter Point module. 2. Select the Import command from the File menu. 3. In the Open dialog, change the filter to *.sp3. 4. Open the directory entitled tutorial\geos3d. 5. Select the file entitled tank.sp3. 6. Click on the Open button. 7. Select the Oblique View macro. A set of points should appear on the screen. Notice that the points are arranged in vertical columns. This hypothetical set of points is meant to represent a set of measurements of contaminant concentration in the vicinity of a leaky underground storage tank. Each column of points corresponds to a borehole or the path of a penetrometer along which concentrations were measured at uniform intervals. The goal of the tutorial is to use the tools for

63 Three-Dimensional Geostatistics 5-3 3D geostatistics in GMS to interpolate from the scatter points to a grid and generate a graphical representation of the plume. 5.4 Displaying Data Colors Next, we will change the display options so that the color of each point is representative of the concentration at the point. 1. Select the Display Options command in the Display menu. 2. Turn on the Data colors option. 3. Select the OK button. 4. Select the Color Ramp Options command from the Data menu. 5. Turn on the Show color legend option. 6. Select the OK button. Notice that most of the values are zero. The nonzero values are all at about the same depth in the holes. This pattern is fairly common when dealing with light non-aqueous phase liquids (LNAPLs) which form a pancake shaped plume and float on the water table. 5.5 Z Magnification Next, we will magnify the z coordinate so that the vertical variation in the data is more apparent. 1. Select the Z Magnification command in the View menu. 2. Enter a value of Select the OK button. 5.6 Creating a Bounding Grid To generate a graphical representation of the contaminant plume, we must first create a grid that bounds the scatter point set. We will then interpolate the data from the scatter points to the grid nodes. The grid will then be used to generate iso-surfaces. To create the grid:

64 5-4 GMS Tutorials 1. Select Bounding Grid from the Scatter Points menu. Notice that the x, y, and z dimensions of the grid are already defined. The default values shown in the dialog cause the grid to extend beyond the scatter points by 10% on each side. 2. Enter 30 for the number of cells in the x direction. 3. Enter 10 for the number of cells in the y direction. 4. Enter 10 for the number of cells in the z direction. 5. Check to ensure that the default grid type is Mesh Centered. Two types of grids are supported in GMS: cell-centered and meshcentered. While cell-centered is appropriate for groundwater models (MODFLOW), the mesh-centered approach is more appropriate when the grid will be used solely for interpolation. 6. Select the OK button. A grid should appear on the screen that just encompasses the scatter point set. 5.7 Simple IDW Interpolation The next step is to select an interpolation scheme. First, we will use the inverse distance weighted interpolation scheme (IDW). 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Inverse distance weighted option. 3. Select the Options button to the right of the Inverse distance weighted option. 4. In the Nodal function section at the top of the dialog, select the Constant option. 5. In the section entitled Computation of interpolation weights, select the Use subset of points option. 6. Select the Subset button in the Computation of interpolation weights section. 7. Select the Use nearest points option and enter 64 for the number of points.

65 Three-Dimensional Geostatistics Select the OK button to exit the Subset Definition dialog. 9. Select the Close button to exit the IDW Interpolation Options dialog. 10. Select the Close button to exit the Interpolation Options dialog. To interpolate to the grid: 1. Select the to 3D Grid command from the Interpolation menu. 2. Enter "idw_const" for the name of the new data set. 3. Select the OK button. 5.8 Displaying Iso-surfaces Now that we have interpolated to the nodes of the 3D grid there are several ways to visualize the contaminant plume. One of the most effective ways is to use iso-surfaces. Iso-surfaces are the three-dimensional equivalent of contour lines. An iso-surface represents a surface of a constant value (contaminant concentration in this case). To define and display iso-surfaces: 1. Switch to the 3D Grid module. 2. Select the Display Options macro. 3. Turn off the Cells option and turn on the Grid shell, Fringes, and Isosurfaces options. 4. Select the Options button to the right of the Iso-Surfaces option. 5. In the first edit field in the list of values, type Turn on the Cap option between values 1 & Select the OK button to exit the Iso-Surface Options dialog. 8. Select the OK button to exit the Display Options dialog. You should now see a wireframe representation of the iso-surface. To generate a shaded image: 1. Select the Shading Options command from the Display menu. 2. Select the Hidden surface option, and turn on the following options: Use light source, Smooth features, and Overlay edges.

66 5-6 GMS Tutorials 3. Select the OK button. 4. Select the Shade macro. A color shaded plot of the iso-surface should appear on the screen. 5.9 Interior Edge Removal A series of edges are draped over the iso-surface plot. These edges represent the intersection of the iso-surface with the grid cells. The edges are displayed to help the user visualize the spatial variation or relief in the iso-surface. However, it is sometimes useful to inhibit the display of the edges in some areas. For example, in the regions where the plume intersects the grid the isosurface is flat. We will turn off the display of the edges in this area since they provide little benefit. 1. Select the Iso-Surface Options command from the Data menu. 2. At the bottom of the dialog, select the Interior edge removal option. This removes the edges between adjacent planar facets that are coplanar. 3. Select the OK button. 4. Select the Shade macro Fringe Specified Range You may have noticed that the shell of the iso-surface is all one color, but the interior of the iso-surface (where the iso-surface intersects the boundary of the grid) varies in color according to the contaminant concentration. We can change the display options so that the color variation in this region is more distinct. 1. Select the Fringe Options command from the Data menu. 2. Select the Color fringe specified range option. 3. Enter 3000 for the Minimum fringe value. 4. Enter 9000 for the Maximum fringe value. 5. Select the OK button.

67 Three-Dimensional Geostatistics Select the Shade macro Using the Z Scale Option The scatter points we are using were obtained along vertical traces. In such cases, the distances between scatter points along the vertical traces are significantly smaller than the distances between scatter points along the horizontal plane. This disparity in scaling causes clustering and can be a source of poor results in some interpolation methods. The effects of clustering along vertical traces can be minimized using the z scale option in the Interpolation Options dialog. The z coordinate of each of the scatter points is multiplied by the z scale parameter prior to interpolation. Thus, if the z scale parameter is greater than 1.0, scatter points along the same vertical axis appear farther apart than they really are and scatter points in the same horizontal plane appear closer than they really are. As a result, points in the same horizontal plane are given a higher relative weight than points along the z axis. This can result in improved accuracy, especially in cases where the horizontal correlation between scatter points is expected to be greater than the vertical correlation (which is typically the case due to horizontal layering of soils or due to spreading of the plume on the top of the water table). To change the z scale option: 1. Switch to the 3D Scatter Point module. 2. Select the Interp. Options command from the Interpolation menu. 3. Change the z scale value to Select the OK button. 5. Select the to 3D Grid command from the Interpolation menu. 6. Enter idw_const2 for the new data set name. 7. Select the OK button. 8. Select the Shade macro. As can be seen, there is now much more correlation in the horizontal direction.

68 5-8 GMS Tutorials 5.12 IDW Interpolation With Gradient Planes As discussed in the Two-Dimensional Geostatistics tutorial, IDW interpolation can often be improved by defining higher order nodal functions at the scatter points. The same is true in three dimensions. Next, we will try IDW interpolation with gradient plane nodal functions. 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Options button to the right of the Inverse distance weighted option. 3. In the Nodal function section at the top of the dialog, select the Gradient plane option. 4. Select the OK button to exit the IDW Interpolation Options dialog. 5. Select the Close button to exit the Interpolation Options dialog. To interpolate to the grid: 1. Select the to 3D Grid command from the Interpolation menu. 2. Enter "idw_gp" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro IDW Interpolation With Quadratic Functions Next, we will try IDW interpolation with quadratic nodal functions. 1. Select the Interp. Options command from the Interpolation menu. 2. Select the Options button to the right of the Inverse distance weighted option. 3. In the Nodal function section at the top of the dialog, select the Quadratic option. 4. In the section entitled Computation of nodal function coefficients, select the Use all points option. 5. Select the OK button to exit the IDW Interpolation Options dialog. 6. Select the Close button to exit the Interpolation Options dialog.

69 Three-Dimensional Geostatistics 5-9 To interpolate to the grid: 1. Select the to 3D Grid command from the Interpolation menu. 2. Enter "idw_quad" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro Other Interpolation Schemes Two other 3D interpolation schemes, natural neighbor interpolation and kriging, are supported in GMS. However, these schemes will not be reviewed in this tutorial. You are encouraged to experiment with these techniques at your convenience Viewing the Plume With a Cross Section While iso-surfaces are effective for displaying contaminant plumes, it is often useful to use color-shaded cross sections to illustrate the variation in the contaminant concentration. Next, we will cut a horizontal cross section through the center of the plume. 1. Switch to the 3D Grid module. 2. Select the Side View macro. 3. Select the Create Cross Section tool. 4. Cut a horizontal cross section through the grid by clicking to the left of the grid, moving the cursor to the right of the grid, and double clicking. Cut the cross section through the middle of the iso-surface. 5. Select the Oblique View macro. Before we shade the cross section, we will turn off the display of the isosurfaces. 1. Select the Display Options macro. 2. Turn off the Iso-surfaces option.

70 5-10 GMS Tutorials 3. Select the OK button. Next, we will set up the display options for the cross-section. 1. Select the Cross Section Options command in the Data menu. 2. Turn on the Interior edge removal option. 3. Turn on the Fringes option. 4. Select the OK button. Finally, we will reset the Fringe options. 1. Select the Fringe Options command in the Data menu. 2. Turn off the Color fringe specified range option. 3. Select the OK button. To shade the image: Select the Shade macro Using the Truncation Option Notice the range of contaminant concentration values shown in the color legend at the upper left corner of the Graphics Window. A large percentage of the values are negative. This occurs due to the fact that a higher order nodal function was used. Both the quadratic and the gradient plane nodal functions infer trends in the data and try to preserve those trends. In some regions of the grid, the values at the scatter points are decreasing as you move away from the center of the plume. This decreasing trend is preserved by the interpolation scheme and the interpolated values approach zero and eventually become negative in some areas. However, a negative concentration does not make sense. This problem can be avoided by turning on the Truncate values option in the Interpolation Options dialog. This option can be used to force all negative values to have a value of zero. 1. Switch to the 3D Scatter Point module. 2. Select the Interp. Options command in the Interpolation menu. 3. Turn on the Truncate values option. 4. Select the Truncate to min/max of active data set option.

71 Three-Dimensional Geostatistics Select the OK button. To interpolate to the grid: 1. Select the to 3D Grid command from the Interpolation menu. 2. Enter "idw_quad_trunc" for the name of the new data set. 3. Select the OK button. 4. Select the Shade macro. Notice that the minimum value listed in the color legend is zero Setting up a Moving Cross Section Film Loop It is possible to create several cross sections at different locations in the grid to illustrate the spatial variation of the plume. This process can be automated using the Film Loop utility in GMS. A film loop animation can be generated showing a color shaded cross section moving through the grid Display Options Before setting up the film loop, we will first delete the existing cross section, turn off the color legend, and reset the fringe range. 1. Switch to the 3D Grid module. 2. Select the Select Cross Sections tool. 3. Select the cross section by clicking on the diamond shaped symbol displayed on the cross section. 4. Select the Delete command from the Edit menu. 5. Select the OK button to confirm the deletion. 6. Select the Color Ramp Options command from the Data menu. 7. Turn off the Show color legend option. 8. Select the OK button. 9. Select the Fringe Options command from the Data menu. 10. Select the Color fringe specified range option.

72 5-12 GMS Tutorials 11. Enter for the Minimum fringe value. 12. Enter for the Maximum fringe value. 13. Select the OK button Setting up the Film Loop To set up the film loop: 1. Select the Film Loop command from the Data menu. 2. Select the Setup button. 3. Turn on the Animate cutting plane option. 4. Turn on the Z cutting plane. 5. Select the OK button Playing Back the Film Loop You should see some images appear on the screen. These are the frames of the film loop which are being generated. Once they are all generated you can play them back at a high speed. When the hourglass cursor disappears: 1. Select the Play button to begin the animation. You may wish to experiment with some of the other playback options. 2. After viewing the animation, select the Stop button to stop the animation Setting up a Moving Iso-Surface Film Loop Another effective way to visualize the plume model is to generate a film loop showing a series of iso-surfaces corresponding to different iso-values. To set up the film loop: 1. Select the Setup button in the Film Loop dialog. 2. Turn off the Animate cutting plane option. 3. Turn on the Animate iso-surface option. 4. Enter for the Begin value.

73 Three-Dimensional Geostatistics Enter for the End value. 6. Select the Cap above option. 7. Select the Display values option. 8. Select the OK button. 9. Once the images are generated, use the playback options to view the film loop. 10. After viewing the film loop, select the Stop button to stop the animation. 11. Select the Done button to exit the Film Loop dialog Deleting the Grid and Scatter Point Data To delete all data currently in memory: 1. Select the New command in the File menu. 2. Select No to confirm the deletion Conclusion This concludes the Three-Dimensional Geostatistics tutorial. If you were originally running in normal mode and switched to demo mode to complete this tutorial, you can switch back to normal mode as follows: 1. Select the Normal Mode command from the File menu. 2. Select the OK button at the prompt. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

74

75 6 MODFLOW - Grid Approach CHAPTER 6 MODFLOW - Grid Approach Two approaches can be used to construct a MODFLOW simulation in GMS: the grid approach and the conceptual model approach. The grid approach involves working directly with the 3D grid and applying sources/sinks and other model parameters on a cell-by-cell basis. The conceptual model approach involves using the GIS tools in the Map module to develop a conceptual model of the site being modeled. The data in the conceptual model are then copied to the grid. The grid approach to MODFLOW pre-processing is described in this tutorial. In most cases, the conceptual model approach is more efficient than the grid approach. However, the grid approach is useful for simple problems or academic exercises where cell-by-cell editing is necessary. It is not necessary to complete this tutorial before beginning the MODFLOW - Conceptual Model Approach tutorial. 6.1 Description of Problem The problem we will be solving in this tutorial is shown in Figure 6.1. This problem is a modified version of the sample problem described near the end of the MODFLOW Reference Manual. Three aquifers will be simulated using three layers in the computational grid. The grid covers a square region measuring ft by ft. The grid will consist of 15 rows and 15 columns, each cell measuring 5000 ft by 5000 ft in plan view. For simplicity, the elevation of the top and bottom of each layer will be flat. The hydraulic conductivity values shown are for the horizontal direction. We will use values equal to one fifth of these amounts for the vertical direction.

76 6-2 GMS Tutorials Flow into the system is due to infiltration from precipitation and will be defined as recharge in the input. Flow out of the system is due to buried drain tubes, discharging wells (not shown on the diagram), and a lake which is represented by a constant head boundary on the left. Starting heads will be set equal to zero, and a steady state solution will be computed. Const Head = 0 ft in column 1 of layers 1 & 2 Drain Recharge = ft/d Unconfined Confined Confined Layer 1: K = 50 ft/d, top elev. = 200 ft, bot elev. = -150 ft Layer 2: K = 3 ft/d, top elev. = -150 ft, bot elev. = -400 ft Layer 3: K = 7 ft/d, top elev. = -400 ft, bot elev. = -700 ft Figure 6.1 Sample Problem to be Solved. 6.2 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state. 6.3 Required Modules/Interfaces This tutorial utilizes the following components of the GMS interface: The 3D Grid module The MODFLOW interface You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If you have licensed and enabled each of the listed items on your version of GMS, you can proceed to complete the tutorial in normal mode. If not, you will need to obtain an updated password or hardware lock before continuing. The

77 MODFLOW - Grid Approach 6-3 tutorial cannot be completed in demo mode because the ability to save files is required. 6.4 Creating the Grid The first step in solving the problem is to create the 3D finite difference grid. 1. Switch to the 3D Grid module. 2. Select the Create Grid command from the Grid menu. 3. In the section entitled X-dimension, enter for the Length value, and 15 for the Number cells value. 4. In the section entitled Y-dimension, enter for the Length value, and 15 for the Number cells value. 5. In the section entitled Z-dimension, enter for the Length value, and 3 for the Number cells value. The thickness of the cells in the z direction does not affect the MODFLOW computations. The dimension we have entered was chosen to make the cells appear square when displayed prior to entering the layer elevation data. 6. Select the OK button. The grid should appear in your window in plan view. A simplified representation of the grid should also appear in the Mini-Grid Plot in the Tool Palette. 6.5 Initializing the MODFLOW Simulation The next step in setting up the model is to initialize the MODFLOW simulation. Select the New Simulation command from the MODFLOW menu. 6.6 The Basic Package The input to MODFLOW is subdivided into packages. Some of the packages are optional and some are required. One of the required packages is the Basic package. We will begin with this package:

78 6-4 GMS Tutorials Select the Basic Package command from the MODFLOW menu Titles First, we will enter the titles (optional): 1. For the first line of the heading, enter: "GMS MODFLOW Tutorial Grid Approach". 2. For the second line of the heading, enter your name and the current date Packages Next, we will select the packages. Select the Packages button. The packages dialog is used to specify which of the packages we will be using to set up the model. The Basic package is always used and, therefore, it cannot be turned off. To select the other packages: 1. Select the Recharge package. 2. Select the Drain package. 3. Select the Well package. 4. In the Solver section, select the Strongly Implicit Procedure package. 5. Select the OK button to exit the Packages dialog Units At this point, we can define the units used in the model. The units we choose will be applied to edit fields in the GMS interface to remind of the proper units for each parameter. 1. Select the Units button. 2. Enter ft for the length unit and d for the time unit. We will ignore the other units (they are not used for flow simulations). 3. Select the OK button.

79 MODFLOW - Grid Approach The IBOUND Array The next step is to set up the IBOUND array. The IBOUND array is used to designate each cell as either active (IBOUND>0), inactive (IBOUND=0), or constant head (IBOUND<0). For our problem, all cells will be active, except for the first two layers in the leftmost column, which will be designated as constant head. Select the IBOUND button. The IBOUND dialog displays the values of the IBOUND array in a spreadsheet-like fashion, one layer at a time. The edit field in the upper left corner of the dialog can be used to change the current layer. For our problem, we need all of the values in the array to be greater than zero, except for the left column of the top two layers, which should be less than zero. By default, the values in the array should already be greater than zero. Therefore, all we need to do is change the values for the constant head cells. This can be accomplished by entering a value of -1 for each of the thirty constant head cells. However, there is another way to edit the IBOUND array that is much simpler for this case. This method will be described later in the tutorial. For now we will leave all of the cells active. Select the OK button to exit the IBOUND dialog Starting Heads The next step is to set up the Starting Heads array. Select the Starting Heads button. The Starting Heads array is used to establish an initial head value when performing a transient simulation. Since we are computing a steady state simulation, the initial head for each cell shouldn t make a difference in the final solution. However, the closer the starting head values are to the final head values, the more quickly MODFLOW will converge to a solution. Furthermore, for certain types of layers, if the starting head values are too low, MODFLOW may interpret the cells as being dry. For the problem we are solving, an initial value of zero everywhere should suffice. The Starting Heads array is also used to establish the head values associated with constant head cells. For our problem, the constant head values are zero. Since all of the starting head values are already zero by default, we don t need to make any changes. Select the OK button to exit the Starting Heads dialog.

80 6-6 GMS Tutorials Exiting the Dialog This completes the input for this dialog. Select the Close button to exit the MODFLOW Basic Package dialog. 6.7 Assigning IBOUND Values Directly to Cells As mentioned above, the IBOUND values can be entered through the IBOUND Array dialog. In some cases, it is easier to assign values directly to cells. This can be accomplished using the Cell Attributes command. Before using the command, we must first select the cells in the leftmost column of the top two layers Viewing the Left Column To simplify the selection of the cells, we will change the display so that we are viewing the leftmost layer. Choose the View the J Axis macro. Notice that we are now viewing column number one (the leftmost column) Selecting the Cells To select the cells: 1. Choose the Select Cells tool. 2. Drag a box around all of the cells in the top two layers of the grid Changing the IBOUND Value To edit the IBOUND value: 1. Select the Cell Attributes command from the MODFLOW menu. 2. Enter a value of -1 for the IBOUND value. 3. Select the OK button to exit the Cell Attributes dialog. 4. To unselect the selected cells, click anywhere in the Graphics Window outside the grid. 5. Select the View the K Axis macro.

81 MODFLOW - Grid Approach 6-7 Notice that a symbol is displayed in the cells we edited, indicating that the cells are constant head cells Checking the Values To ensure that the IBOUND values were entered correctly: 1. Select the Basic Package command from the MODFLOW menu. 2. Select the IBOUND button. 3. Choose the up arrow to the right of the layer field in the upper left corner of the dialog to cycle through the layers. Notice that the leftmost column of cells in the top two layers all have a value of -1. Most of the MODFLOW input data can be edited in GMS using either a spreadsheet-like dialog such as this, or by selecting a set of cells and entering a value directly, whichever is most convenient. 1. Select the OK button to exit the IBOUND Array dialog. 2. Select the Close button to exit the MODFLOW Basic Package dialog. 6.8 The BCF Package The next step in setting up the model is to enter the data for the block-centered flow (BCF) package. The BCF package is required for all simulations. The block-centered flow package computes the conductances between each of the grid cells and sets up the finite difference equations for the cell to cell flow. To enter the BCF data: Select the BCF Package command from the MODFLOW menu Layer Types The options on the right side of the dialog are used to define the layer type and conductance data for each layer. For our problem, we have three layers. The top layer is unconfined, and the bottom two layers are confined. Since this is the default, we don t need to make any changes to the layer types Layer Parameters The buttons in the lower right portion of the dialog are for entering the parameters necessary for computing the cell to cell conductances.

82 6-8 GMS Tutorials MODFLOW requires a set of parameters for each layer depending on the layer type. The parameters include transmissivity and leakance that are a function of the layer thicknesses. By default, GMS uses the "true layer" approach for defining layer data. The user enters the top and bottom elevation and the vertical and horizontal hydraulic conductivity for each layer. When the data are written to the MODFLOW file, GMS automatically computes the required parameters for each layer Top Layer First, we will enter the data for the top layer: 1. Select the Top Elevation button. 2. Select the Constant -> Layer button. 3. Enter a value of Select the OK button. 5. Select the OK button to exit the Top Elevation dialog. Repeat this process to enter the following values for the top layer: Parameter Bottom Elevation Horizontal Hydraulic Conductivity Vertical Hydraulic Conductivity Value -150 ft 50 ft/d 5 ft/d Middle Layer Next, we will enter the data for the middle layer: Select the up arrow to the right of the layer edit field at the top of the dialog. Enter the following values for layer 2: Parameter Bottom Elevation Horizontal Hydraulic Conductivity Vertical Hydraulic Conductivity Value -400 ft 3 ft/d 0.5 ft/d Bottom Layer Switch to layer 3 and enter the following values:

83 MODFLOW - Grid Approach 6-9 Parameter Bottom Elevation Horizontal Hydraulic Conductivity Vertical Hydraulic Conductivity This completes the data entry for this dialog. Value -700 ft 7 ft/d 1.5 ft/d Select the Close button to exit the MODFLOW Block Centered Flow dialog. 6.9 The Recharge Package Next, we will enter the data for the Recharge package. The Recharge package is used to simulate recharge to an aquifer due to rainfall and infiltration. To enter the recharge data: 1. Select the Recharge Package command from the MODFLOW menu. 2. Select the Constant -> Array button. 3. Enter a value of Select the OK button. 5. Select the OK button to exit the Recharge Package dialog The Drain Package We will now define the row of drains in the top layer of the model. To define the drains, we must first select the cells where the drains are located, and then select the Point Sources/Sinks command Selecting the Cells The drains are located in the top layer (layer 1). Since this is the current layer, we don t need to change the view. We need to select the cells on columns 2-10 of row 8. To select the cells: 1. Choose the Select Cells tool. 2. Select the cell at i=8, j=2. Notice that as you move the cursor across the grid, the ijk indices of the cell beneath the cursor are displayed in the Edit Window at the bottom of the screen.

84 6-10 GMS Tutorials 3. Hold down the Shift key to invoke the multi-select mode and select the cells on columns 3-10 of the same row as the cell you have already selected (Figure 6.2). Y Z X Figure 6.2 Cells to be Selected Assigning the Drains To assign drains to the cells: 1. Select the Point Sources/Sinks command from the MODFLOW menu. 2. In the Drain section, select the Add option. This adds a new instance of a drain to each of the selected cells. At this point we must enter an elevation and a conductance for the selected drains. The drains all have the same conductance but the elevations are not all the same. We will leave the elevation at the default value for now and change the elevations later using the Drain Package dialog. 1. Enter a value of 80,000 for the conductance. 2. Select the OK button. 3. Unselect the cells by clicking anywhere outside the grid.

85 MODFLOW - Grid Approach Assigning the Drain Elevations At this point, we could select the drain cells one at a time and use the Cell BC dialog to edit the elevations. However, once the drains are defined, it is often easier to edit the values using the Drain Package dialog. 1. Select the Drain Package command from the MODFLOW menu. 2. Enter the following values for the elevations of the drains: row (i) col (j) lay (k) elev Select the OK button The Well Package Next, we will define several wells by selecting the cells where the wells are located and using the Point Sources/Sinks command Top Layer Wells Most of the wells are in the top layer but some are in the middle and bottom layers. We will define the wells in the top layers first. 1. While holding down the Shift key, select the following cells: row (i) col (j) lay (k) These cells are shown in Figure Select the Point Sources/Sinks command from the MODFLOW menu.

86 6-12 GMS Tutorials 3. In the Well section, select the Add button. 4. Enter a Flow value of (the minus sign signifies extraction). 5. Select the OK button. 6. Unselect the cells by clicking anywhere outside the grid. Constant Head Cells Drain Cells Select these cells Y Z X Figure 6.3 Cells to be Selected on Top Layer Middle Layer Wells Next, we will define some wells on the middle layer. First, we need to view the middle layer. Select the Decrement button in the Mini-Grid Plot. To select the cells: 1. While holding down the Shift key, select the following cells: row (i) col (j) lay (k) These cells are shown in Figure Select the Point Sources/Sinks command from the MODFLOW menu.

87 MODFLOW - Grid Approach In the Well section, select the Add button. 5. Enter a Flow value of Select the OK button. 7. Unselect the cells by clicking anywhere outside the grid. Constant Head Cells Select these cells Y Z X Figure 6.4 Cells to be Selected on Middle Layer Bottom Layer Well Finally, we will define a single well on the bottom layer. To view the bottom layer: Select the Decrement button in the Mini-Grid Plot. To select the cell: 1. Select the following cell: row (i) col (j) lay (k) The cell is shown in Figure Select the Point Sources/Sinks command from the MODFLOW menu.

88 6-14 GMS Tutorials 4. In the Well section, select the Add button. 5. Enter a Flow value of Select the OK button. 7. Unselect the cells by clicking anywhere outside the grid. Select this cell Y Z X Figure 6.5 Cell to be Selected on Bottom Layer. Now that all of the wells have been defined, we can go back to the top layer. Select the Increment button twice in the Mini-Grid Plot Saving the Simulation Now we are ready to save the simulation and run MODFLOW. 1. Select the Save As command in the MODFLOW menu. 2. Move to the directory titled tutorial\modfgrid 3. Change the file name to gridmod.mfs. 4. Select the Save button.

89 MODFLOW - Grid Approach Running MODFLOW We are now ready to run MODFLOW: 1. Select the Run MODFLOW command from the MODFLOW menu. 2. Select the OK button. At this point MODFLOW is launched in a new window. The super file name is passed to MODFLOW as a command line argument. MODFLOW opens the file and begins the simulation. As the simulation proceeds, you should see some text output in the window reporting the solution progress. When the solution is finished, close the window and return to GMS Viewing the Solution We are now ready to view the solution. 1. Select the Read Solution command from the MODFLOW menu. 2. Select the OK button. At this point you should see a set of head contours for the top layer Changing Layers To view the solution on the middle layer: Select the Decrement button in the Mini-Grid Plot. To view the solution on the bottom layer: Select the Decrement button. To return to the top layer: Select the Increment button twice Color Fill Contours You can also display the contours using a color fill option. 1. Select the Contour Options command in the Data menu. 2. In the lower left section of the dialog, select the Color fill between contours option.

90 6-16 GMS Tutorials 3. Select the OK button Color Legend Next, we will display a color legend. 1. Select the Color Ramp Options command in the Data menu. 2. In the upper right corner of the dialog, select the Show color legend option. 3. Select the OK button Conclusion This concludes the MODFLOW - Basic tutorial. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

91 7 MODFLOW - Conceptual Model Approach CHAPTER 7 MODFLOW - Conceptual Model Approach Two approaches can be used to construct a MODFLOW simulation in GMS: the grid approach or the conceptual model approach. The grid approach involves working directly with the 3D grid and applying sources/sinks and other model parameters on a cell-by-cell basis. The steps involved in the grid approach are described in the previous tutorial entitled MODFLOW - Grid Approach. The conceptual model approach involves using the GIS tools in the Map module to develop a conceptual model of the site being modeled. The location of sources/sinks, layer parameters such as hydraulic conductivity, model boundaries, and all other data necessary for the simulation can be defined at the conceptual model level. Once this model is complete, the grid is generated and the conceptual model is converted to the grid model and all of the cell-by-cell assignments are performed automatically. The steps involved in performing a MODFLOW simulation using the conceptual model approach are described in this tutorial. It is not necessary to complete the MODFLOW - Grid Approach tutorial before completing this tutorial. 7.1 Description of Problem The problem we will be solving for this tutorial is illustrated in Figure 7.1a. The site is located in East Texas. We will assume that we are evaluating the suitability of a proposed landfill site with respect to potential groundwater contamination. The results of this simulation will be used as the flow field for a particle tracking and a transport simulation in the MODPATH tutorial and the MT3DMS tutorial.

92 7-2 GMS Tutorials North Limestone Outcropping Well #1 Proposed Landfill Site Well #2 Creek beds River (a) River River Upper Sediments Limestone Bedrock Lower Sediments (b) Figure 7.1 Site to be Modeled in This Tutorial. (a) Plan View of Site. (b) Typical North-South Cross Section Through Site. We will be modeling the groundwater flow in the valley sediments bounded by the hills to the north and the two converging rivers to the south. A typical north-south cross section through the site is shown in Figure 7.1b. The site is underlain by limestone bedrock which outcrops to the hills at the north end of the site. There are two primary sediment layers. The upper layer will be modeled as an unconfined layer and the lower layer will be modeled as a confined layer. The boundary to the north will be a no-flow boundary and the remaining boundary will be a specified head boundary corresponding to the average stage of the rivers. We will assume the influx to the system is primarily through

93 MODFLOW - Conceptual Model Approach 7-3 recharge due to rainfall and run-on. There are some creek beds in the area which are sometimes dry but occasionally flow due to influx from the groundwater. We will represent these creek beds using drains. There are also two production wells in the area that will be included in the model. NOTE: Although the site modeled in this tutorial is an actual site, the landfill and the hydrogeologic conditions at the site have been fabricated. The stresses and boundary conditions used in the simulation were selected to provide a simple yet broad sampling of the options available for defining a conceptual model. 7.2 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state. 7.3 Required Modules/Interfaces This tutorial utilizes the following components of the GMS interface: The 3D Grid module The 2D Scatter Point module The Map module The MODFLOW interface You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If you have licensed and enabled each of the listed items on your version of GMS, you can proceed to complete the tutorial in normal mode. If not, you will need to obtain an updated password or hardware lock before continuing. The tutorial cannot be completed in demo mode because the ability to save files is required. 7.4 Importing the Background Image The first step in setting up the simulation is to import a digital image of the site being modeled. This image was created by scanning a portion of a USGS quadrangle map on a desktop scanner. The image was saved from the scanning software to a TIFF file using the "packbits" compression option. The

94 7-4 GMS Tutorials image was imported to GMS, registered, and a GMS project file was saved. To read in the image, we will open the project file. Once the image is imported to GMS, it can be displayed in the background as a guide for on screen digitizing and placement of model features Reading the Image To import the image: 1. Select the Open command from the File menu. 2. Locate and open the directory entitled tutorial\modfmap. 3. Select the file entitled start.gpr. 4. Choose the Open button. You should see a message indicating that the image is being resampled. Eventually the image should appear. Now that the image is imported, it will appear each time the screen is refreshed. All other objects are drawn on top of the image. The image only appears in plan view. You are actually viewing only a portion of the complete TIFF image. It is possible to pan and zoom and resample the TIFF image to view a different region or to view at a different resolution. More information on manipulating TIFF images can be found in the GMS Reference Manual Image File vs. TIFF File The project you just opened included a file called an "image" file. It is not the file containing the TIFF image. The TIFF file is called "easttex.tif" and is located in the same directory as the image file. When a TIFF file is first imported it must be registered. Registering a TIFF file involves selecting three points on the image and entering the real world coordinates of those points. These points are used to stretch and position the image when it is drawn on the screen so that it is drawn in the correct location. Once a TIFF image is registered, the registration data and the name of the TIFF file are saved to an image file. From that point on, the TIFF image can be imported and registered in one easy step by opening the image file. The image we are using in this tutorial was registered previously and the registration data were saved to a file named "start.img" when the project was saved. 7.5 Feature Objects We are now ready to begin constructing the conceptual model. Conceptual models are constructed using feature objects in the Map module. Feature

95 MODFLOW - Conceptual Model Approach 7-5 objects in GMS have been patterned after Geographic Information Systems (GIS) objects and include points, nodes, arcs, and polygons (Figure 7.2). Points are xy locations that are not attached to an arc. Points have unique ids and can be assigned attributes. Points are typically used to represent wells. Arcs are sequences of line segments or edges which are grouped together as a single "polyline" entity. Arcs have unique ids and can be assigned attributes. Arcs are grouped together to form polygons or are used independently to represent linear features such as rivers. The two end points of an arc are called "nodes" and the intermediate points are called "vertices". Nodes have unique ids and can be assigned attributes. Vertices are used solely to define the geometry of the arc. Polygons are a group of connected arcs that form a closed loop. A polygon can consist of a single arc or multiple arcs. If two polygons are adjacent, the arc(s) forming the boundary between the polygons is shared (not duplicated). Feature objects can be grouped into coverages. Each coverage represents a particular set of data. Our conceptual model will consist of three coverages: a coverage defining the model boundary and the location of the sources/sinks, a coverage defining the recharge zones, and a coverage defining the zones of hydraulic conductivity. The bottom elevations for the aquifer will be defined by interpolating from a set of observation well measurements. Point Node Vertex Arc Polygons Figure 7.2 Feature Objects. 7.6 Building the Local Source/Sink Coverage The first step in building the conceptual model is to construct the local sources/sinks coverage. This coverage defines the boundary of the region being modeled and it defines local sources/sinks including wells, rivers, drains, and general head boundaries. Coverages in GMS are assigned a "coverage type" corresponding to the intended use of the coverage. The attributes which can be assigned to the feature objects in a coverage depend on the coverage type. When GMS is first

96 7-6 GMS Tutorials launched, a default empty coverage is created. This coverage is a "general" type coverage. Before creating the feature objects, we will change the coverage type to a local source/sink type. 1. Switch to the Map module. 2. Select the Coverages command in the Feature Objects menu. 3. Change the Default elevation to 700. This elevation is assigned to all new objects and affects how the objects are displayed in oblique view. 4. Change the name of the coverage from "default coverage" to "Sources/Sinks". 5. Change the Coverage type to MODF/MT3D/MODP. 6. Select the Options button. 7. Check to ensure that the coverage type is MODF/MT3D local sources/sinks (this should be the default MODFLOW coverage type). 8. Select the OK button to return to the Coverages dialog Defining the Units At this point, we can also define the units used in the conceptual model. The units we choose will be applied to edit fields in the GMS interface to remind us of the proper units for each parameter. 4. Select the Units button. 5. Enter ft for the length unit and d for the time unit. We will ignore the other units (they are not used for flow simulations). 6. Select the OK button. 7. Select OK again to exit the Coverages dialog Defining the Boundary The next step is to define the outer boundary of the model. We will do this by creating an arc which forms a closed loop around the site. 1. Select the Create Arc tool. 2. Begin the arc by clicking once on the left (west) side of the model at the location shown in Figure 7.3.

97 MODFLOW - Conceptual Model Approach Create the arc by proceeding around the boundary of the site in a counter-clockwise direction and clicking on a sequence of points around the boundary. Don t worry about the spacing or the exact location of the points; just use enough points to define the approximate location of the boundary. The boundary on the south and east sides of the model should coincide with the rivers. The boundary along the top should coincide to the limestone outcropping as shown in Figure Double click on the point where you began to end the arc. Note: As you are clicking on the points, if you make a mistake and wish to back up a point or two, press the Backspace key. If you wish to abort the arc and start over, press the ESC key. (e) Double-click here to end. (d) Click points along limestone outcropping. (a) Click here to begin. (c) Click points along this river. (b) Click points along this river. Figure 7.3 Creating the Boundary Arc Copying the Boundary Since this arc defines the boundary of the model, it is useful to use this same boundary in the other coverages we will be creating. Thus, we will save a copy of this arc in a set of coverages for later use. First, we will create a coverage for hydraulic conductivity for each layer. 1. Select the Coverages command in the Feature Objects menu. 2. Select the Copy command. 3. Change the name of the new coverage to "Layer 1". 4. Select the Options button.

98 7-8 GMS Tutorials 5. Change the Coverage type to MODF/MT3D/MODP layer attributes. 6. Select the OK button. 7. With the Layer 1 coverage still highlighted, select the Copy command again. 8. Change the name of the new coverage to "Layer 2". 9. Select the Options button. 10. Change the Coverage type to MODF/MT3D/MODP layer attributes. 11. In the middle of the dialog, change the Assign from layer and to layer fields to 2 and 2 (this will associate the coverage with layer 2). 12. Select the OK button. Next, we will create a coverage for the recharge polygons. Finally: 1. Select the Copy command. 2. Change the name of the new coverage to "Recharge". 3. Select the Options button. 4. Change the Coverage type to MODF/MT3D areal attributes. 5. Select the OK button. 1. (IMPORTANT STEP!) Select the Sources/Sinks coverage so that it will be the active coverage when exiting the dialog. All editing is done to the active coverage. 2. Select the OK button to exit the Coverages dialog Defining the Specified Head Arcs The next step is to define the specified head boundary along the south and east sides of the model. Before doing this, however, we must first split the arc we just created into three arcs. One arc will define the no-flow boundary along the top and the other two arcs will define the two rivers. An arc is split by selecting one or more vertices on the arc and converting the vertices to nodes. 1. Select the Select Vertices tool.

99 MODFLOW - Conceptual Model Approach Select the two vertices shown in Figure 7.4. Vertex #1 is located at the junction of the two rivers. Vertex #2 is located at the top of the river on the east side of the model. To select both vertices at once, select the first vertex and then hold down the Shift key while selecting the other vertex. 3. Select the Vertices <-> Nodes command in the Feature Objects menu. Vertex #2 Vertex #1 Figure 7.4 Convert Vertices to Nodes. Now that we have defined the three arcs, we will specify the two arcs on the rivers as specified head arcs. 1. Select the Select Arcs tool. 2. Select the arcs on the south and east sides of the model by selecting one arc and holding down the Shift key while selecting the other arc. 3. Select the Attributes command in the Feature Objects menu. 4. Select the Specified Head type. 5. At the bottom of the dialog, change the second edit field to 2 so that the head boundary applies to both layers. 6. Select the OK button. 7. Click anywhere on the model other than on the arcs to unselect them. Note that the color of the arcs has changed indicating the type of the arc.

100 7-10 GMS Tutorials The next step is to define the head at the nodes at the ends of the arcs. The head along a specified head arc is assumed to vary linearly along the length of the arc. 1. Select the Select Points/Nodes tool. 2. Double click on the node on the west (left) end of the arc on the southern (bottom) boundary. 3. Enter a constant value for head of Select the OK button. In a similar fashion, assign a value of to the node at the junction of the two rivers and a value of to the node at the top of the arc on the east boundary of the model Defining the Drain Arcs At this point, we will enter the arcs at the locations of the creek beds to define the drains. 1. Select the Create Arc tool. 2. Create the arc labeled as arc #1 in Figure 7.5. Start by clicking on the bottom arc, create the arc by clicking points along the creek bed, and end the arc by double clicking on the top arc. Notice that when you click in the vicinity of a vertex on an existing arc or on the edge of an arc, GMS automatically snaps the arc you are creating to the existing arc and makes a node at the junction of the two arcs. 3. Create the arcs labeled arc #2 and arc #3 in Figure 7.5 the same way you made arc #1.

101 MODFLOW - Conceptual Model Approach 7-11 Arc #1 Arc #3 Arc #2 Figure 7.5 The Drain Arcs. Next, we will define the arcs as drains and assign the conductance and elevation to the arcs. 1. Select the Select Arcs tool. 2. Select all of the drain arcs by clicking on the arcs while holding down the Shift key. 3. Select the Attributes command in the Feature Objects menu. 4. Select the Drain option. 5. Enter a conductance of This represents a conductance per unit length value. GMS automatically computes the appropriate cell conductance value when the drains are assigned to the grid cells. 6. Select the OK button. The elevations of the drains are specified at the nodes of the arcs. The elevation is assumed to vary linearly along the arcs between the specified values. 1. Select the Select Points/Nodes tool. 2. Double click on each of the nodes at the end points of the arcs and assign the elevations as shown in Figure 7.6.

102 7-12 GMS Tutorials Nodes 2, 4 & 6 are connected to both drain and specified head arcs. When assigning the attributes for these nodes, you will notice that both specified head and drain attributes can be edited for the nodes. To edit the drain elevation, select the drain option in the list box in the lower left section of the Attributes dialog. Node 1 Node 5 Node 2 Node 3 Node 4 Node 6 Node Elevation Figure 7.6 Elevations for Drain Nodes Building the polygons With the local sources/sinks type coverage, the entire region to be modeled must be covered with non-overlapping polygons. This defines the active region of the grid. In most cases, all of the polygons will be variable head polygons (the default). However, other polygons may be used. For example, to model a lake, a general head polygon can be used. The simplest way to define the polygons is to first create all of the arcs used in the coverage and then select the Build Polygons command. This command searches through the arcs and creates a polygon for each of the closed loops defined by the arcs. These polygons are variable head by default but may be converted to other types by selecting the polygons and using the Attributes command. Now that all of the arcs in the coverage have been created, we are ready to construct the polygons. All of our polygons will be variable head polygons. 1. Select the Build Polygons command from the Feature Objects menu. 2. When you are asked if you wish to build the polygons using all arcs, select OK.

103 MODFLOW - Conceptual Model Approach 7-13 Even though the polygons are created, there is no visible difference in the display. You can view the polygons if you wish by selecting the Display Options command in the Feature Objects menu and turning on the Polygons (Fill) option Creating the Wells The final step in creating the local sources/sinks coverage is to define the wells. Wells are defined as point type objects. Two wells will be created. 1. Select the Create Point tool. 2. Move the cursor to the approximate location of Well #1 shown in Figure 7.1 and click once with the mouse to create the point. 3. While the new point is selected, type the coordinates (2741.0, ) in the x and y edit fields at the top of the GMS window and hit the Tab or Enter key. 4. Select the Attributes command from the Feature Objects menu. 5. Select the Well option. 6. Enter a constant value of for the flux (pumping) rate. 7. Check to ensure that the well will be applied to layer 1 (this is the default). 8. Select the OK button. In a similar fashion, create the other well at the location ( , ) and assign a pumping rate of 100,000. However, for this well, change the edit fields at the bottom of the dialog so that the well is applied to layer two (change both the edit fields to 2). Grid Refinement A well represents a point of convergence in the groundwater flow and causes steep gradients in the head near the well. In order to accurately model the flow near wells, the grid is typically refined in the vicinity of the wells. This type of refinement can be performed automatically in GMS by assigning refinement data directly to the wells in the conceptual model. 1. Select the Select Points/Nodes tool. 2. Select both wells by clicking on the wells while holding the Shift key.

104 7-14 GMS Tutorials 3. Select the Attributes command in the Feature Objects menu. 4. Select the Refine Point button. 5. Select the Refine grid in X direction option and enter a value of 75.0 for the Base cell size and a value of for the Max cell size. 6. Select the Refine grid in Y direction option and enter a value of 75.0 for the Base cell size and a value of for the Max cell size. 7. Select the OK button twice to exit both dialogs. 7.7 Delineating the Recharge Zones The next step in constructing the conceptual model is to construct the coverage which defines the recharge zones. We will assume that the recharge over the area being modeled is uniform except for the landfill. The recharge in the area of the landfill will be reduced due to the landfill liner system Switching Coverages Before creating the recharge zones, we need to make the Recharge coverage the active coverage. In the Coverage combo box at the top left corner of the window, select the Recharge coverage Creating the Landfill Boundary Next, we will create the arc delineating the boundary of the landfill. To do this, we will first create a closed loop in the form of a rectangle at the approximate location of the landfill. We will then edit the nodes and vertices so that the arc coincides precisely with the boundary of the landfill. 1. Select the Create Arc tool. 2. While watching the cursor coordinates in the bottom left corner of the Edit Window, begin at the lower left corner of the landfill and create a closed rectangular loop by clicking on the following four points representing corners of the landfill. Once you have clicked on the four points, double click on the first point to end the loop. Don't worry about getting the exact coordinates at this point. Simply create the points in the vicinity of the coordinates.

105 MODFLOW - Conceptual Model Approach 7-15 x y Now that the arc is created in the approximate location, we will edit the coordinates of the vertices and nodes to define the precise coordinates. 1. Select the Select Points/Nodes tool. 2. Select the Node in the lower left corner of the landfill. 3. While the node is selected, enter the exact coordinates of the node in the Edit Window. Select the Tab key after entering each coordinate value. 4. Select the Select Vertices tool. 5. Starting with the vertex at the lower right corner of the landfill, select each of the three remaining vertices on the arc and enter the exact coordinates shown in the table above Building the Polygons Now that the arcs are defined, we can build the polygons. 1. Select the Build Polygons command in the Feature Objects menu. 2. When you are asked if you wish to build the polygons using all arcs, select OK Assigning the Recharge Values Now that the recharge zones are defined, we can assign the recharge values. We will assign one value to the landfill polygon, and another value to the remaining polygon. 1. Select the Select Polygons tool. 2. Double click on the landfill polygon. 3. Turn on the Recharge option and enter a constant value of for the recharge rate. Note: This recharge rate is small relative to the rate assigned to the other polygons. The landfill will be capped and lined and thus will

106 7-16 GMS Tutorials have a small recharge value. The recharge essentially represents a small amount of leachate that escapes from the landfill. 4. Select the OK button. 5. Double click on the outer polygon. 6. Turn on the Recharge option and enter a constant value of for the recharge rate. 7. Select the OK button. 7.8 Defining the Hydraulic Conductivity Next we will enter the hydraulic conductivity for each layer. In many cases, you may wish to define multiple polygons defining hydraulic conductivity zones. For the sake of simplicity, we will use a constant value for each layer Top Layer First, we will assign a K value for the top layer. 1. In the Coverage combo box, select the Layer 1 coverage. 2. From the Feature Objects menu select the Build Polygons command and select OK at the prompt. 3. Double click on the polygon 4. Select the Horizonal K option and enter a value of Select the Vertical K option and enter a value of Select the OK button Bottom Layer For the bottom layer: 1. In the Coverage combo box, select the Layer 2 coverage. 2. From the Feature Objects menu select the Build Polygons command and select OK at the prompt. 3. Double click on the polygon

107 MODFLOW - Conceptual Model Approach Select the Horizonal K option and enter a value of Select the Vertical K option and enter a value of Select the OK button. This completes the definition of the coverages in the conceptual model. Before continuing to create the grid, we will make the sources/sinks coverage the active coverage. In the Coverage combo box, select the Sources/Sinks coverage. 7.9 Locating the Grid Frame Now that the coverages are complete, we are ready to create the grid. The first step in creating the grid is to define the location and orientation of the grid using the Grid Frame. The Grid Frame represents the outline of the grid. It can be positioned on top of our site map graphically. 1. Select the Grid Frame command in the Feature Objects menu. 2. Select the New Frame button. 3. Move the boundaries of the Grid Frame by dragging the handles that appear on the corners and the midsides of the Grid Frame with the mouse. Position the boundaries so that they just surround the boundaries of the conceptual model. You may need to move the Grid Frame dialog once or twice as you position the Grid Frame. Note: In some cases, the best fit of the grid to the model is achieved when the grid is rotated. The Grid Frame can be rotated by selecting and dragging the rotation handle (the dot just to the right of the lower right corner of the Grid Frame). The Grid Frame can also be positioned and rotated using the buttons and edit fields in the Grid Frame dialog. If the handles of the grid frame are not visible, you may wish to select the Plan View macro or adjust the values in the edit fields until they become visible. 4. For the Z coordinate, change the Origin to 550 and the Dimension to 200. This provides a set of initial values for the MODFLOW layer elevation arrays. Later, we will interpolate the layer elevations 5. Select the OK button to exit the Grid Frame dialog.

108 7-18 GMS Tutorials 7.10 Creating the Grid Now that the coverages and the Grid Frame are created, we are now ready to create the grid. 1. Select the Map -> 3D Grid command in the Feature Objects menu. Notice that the grid is dimensioned using the data from the Grid Frame. If a Grid Frame does not exist, the grid is defaulted to surround the model with approximately 5% overlap on the sides. Also note that the number of cells in the x and y dimensions cannot be altered. This is because the number of rows and columns and the locations of the cell boundaries will be controlled by the refine point data entered at the wells. 2. Enter a value of 2 for the number of cells in the z direction. 3. Select the OK button Defining the Active/Inactive Zones Now that the grid is created, the next step is to define the active and inactive zones of the model. This is accomplished automatically using the information in the local sources/sinks coverage. Select the Activate Cells in Coverage(s) command from the Feature Objects menu. Each of the cells in the interior of any polygon in the local sources/sinks coverage is designated as active and each cell which is outside of all of the polygons is designated as inactive. Notice that the cells on the boundary are activated such that the no-flow boundary at the top of the model approximately coincides with the outer cell edges of the cells on the perimeter while the specified head boundaries approximately coincide with the cell centers of the cells on the perimeter Initializing the MODFLOW Data Now that the grid is constructed and the active/inactive zones are delineated, the next step is to convert the conceptual model to a grid-based numerical model. Before doing this, however, we must first initialize the MODFLOW data: 1. Switch to the 3D Grid module.

109 MODFLOW - Conceptual Model Approach Select the New Simulation command from the MODFLOW menu Converting the Conceptual Model We are now ready to convert the conceptual model from a high-level feature object-based definition to a grid-based MODFLOW numerical model. 1. Switch to the Map module. 2. Select the Map -> MODFLOW command in the Feature Objects menu. 3. Make sure the All applicable coverages option is selected and select OK. Notice that the cells underlying the drains, wells, and specified head boundaries were all identified and assigned the appropriate sources/sinks. The heads and elevations of the cells were determined by linearly interpolating along the specified head and drain arcs. The conductances of the drain cells were determined by computing the length of the drain arc overlapped by each cell and multiplying that length by the conductance value assigned to the arc. In addition, the recharge and hydraulic conductivity values were assigned to the appropriate cells Interpolating Layer Elevations The final step before we save the model and run MODFLOW is to define the layer elevations and the starting head. With the "true layer" approach used in GMS, top and bottom elevations are defined for each layer regardless of the layer type. For a two layer model, we need to define a layer elevation array for the top of layer one (the ground surface), the bottom of layer one, and the bottom of layer two. It is assumed that the top of layer two is equal to the bottom of layer one. The simplest way to define layer elevations is to import a set of scatter points defining the elevations and interpolate the elevations directly to the layer arrays. In some cases, this is done using one set of scatter points. In this case, we will use two scatter point sets: one for the ground surface and one for the elevations of the bottom of layer one and the bottom of layer two. It is often convenient to use two scatter point sets in this fashion due to the source of the points. Ground surface points are often digitized from a map while layer elevations typically come from borehole data. For most steady state MODFLOW models, a constant value of starting head will lead to a good solution. In some cases, the model stability and speed of

110 7-20 GMS Tutorials convergence can be improved by selecting a set of starting heads that are closer to the final solution. We will use the latter method. Our starting heads will be defined by a surface that is a constant depth below the ground surface Importing the Ground Surface Scatter Points The ground surface scatter points have been entered in a simple text file which can be imported to GMS. The file is in a tabular format with multiple columns and was created with a text editor. The columns include the x and y coordinates and the ground surface elevation. 1. Switch to the 2D Scatter Point module. 2. Select the Import command in the File menu. 3. In the Open dialog, select the *.sp2 filter. 4. Locate and open the directory titled tutorial\modfmap. 5. Select the file titled terrain.sp2. 6. Select the Open button. A set of scatter point symbols should appear on the model Calculating a Starting Head Data Set The starting head values will be defined as a surface parallel to the ground surface at a depth of 10 ft below the ground surface. We can define such a data set using the Data Calculator. Select the Data Calculator command in the Data menu. Note that the available data sets are listed in the top of the dialog. We can create a new dialog simply by typing an expression and referencing each data set by the letter shown in the list. 1. In the Expression field, type "a-10". 2. In the Result field, type "starting head". 3. Select the Compute button. 4. Select the Done button to exit the dialog.

111 MODFLOW - Conceptual Model Approach Interpolating the Heads and Elevations Next, we will interpolate the ground surface elevations and starting heads to the MODFLOW grid. Select the to MODFLOW Layers command in the Interpolation menu. The list on the top left side of the dialog represents the data sets available in the active scatter point set. The list on the top right side lists the MODFLOW layer arrays that can be interpolated to. The dialog is used to associate each of the data sets with the appropriate layer arrays. This is accomplished by selecting an item from each list and selecting the Map button. The list at the bottom shows the relationships that have been mapped. The starting head array is already mapped since the association is obvious from the names used for the data set and the array. We also want to map the ground elevations to the top of layer one. 1. Check to make sure that the "ground_elev" data set and the "Top Elevations Layer 1" array are highlighted. 2. Select the Map button. 3. Select the OK button to perform the interpolation Importing the Layer Elevation Scatter Points Next, we will import the scatter points defining the layer elevations. 1. Select the Import command in the File menu. 2. In the Open dialog, select the *.sp2 filter. 3. Select the file titled "elevs.sp2". 4. Select the Open button. A second set of scatter point symbols should appear on the model Interpolating the Layer Elevations To import the layer elevations: 1. Select the to MODFLOW Layers command in the Interpolation menu. 2. Check to confirm that the mappings are properly selected (the correct mapping should be selected by default). 3. Select the OK button.

112 7-22 GMS Tutorials Adjusting the Display Now that we are finished with the interpolation, we can hide the scatter point sets. 1. Select the Select Scatter Point Sets tool. 2. Drag a box around both of the scatter point set symbols (the pentagons). 3. Select the Hide macro. We will also turn off the grid frame. 1. Switch to the Map module. 2. Select the Display Options command in the Display menu. 3. Turn off the Grid frame option. 4. Select the OK button Viewing the Model Cross Sections To check the interpolation, we will view a cross section. 1. Switch to the 3D Grid module. 2. Select a cell somewhere near the center of the model. 3. Select the View J Axis macro. To get a better view of the cross section, we will increase the z magnification. 1. Select the Z Magnification command from the View menu. 2. Enter a value of 5 for the Z magnification factor. 3. Select the OK button. You may wish to use the arrow buttons in the Tool Palette to view different columns in the grid. Note that on the right side of the cross section, the bottom layer pinches out and the bottom elevations are greater than the top elevations. This must be fixed before running the model.

113 MODFLOW - Conceptual Model Approach Fixing the Elevation Arrays GMS provides a convenient set of tools for fixing layer array problems. These tools are located in the Model Checker. 1. Select the Check Simulation command in the MODFLOW menu. 2. Select the Run Check button. 3. Select the Fix Layer Errors button at the top of the dialog. Notice that many errors were found for layer two. There are several ways to fix these layers. We will use the Truncate to bedrock option. This option makes all cells below the bottom layer inactive. 1. Select the Truncate to bedrock option. 2. Select the Fix Affected Layers button (it does not matter which layer is selected, all layers that are affected will be fixed). 3. Select the OK button to exit the Fix Layer Errors dialog. 4. Select the Done button to exit the Model Checker. Notice that the layer errors have been fixed. Another way to view the layer corrections is in plan view. 1. Switch to plan view by selecting the View K Axis macro. 2. In the mini-grid display, select the down arrow to view the second layer. Notice that the cells at the upper (Northern) edge of the model in layer two are inactive. Switch back to the top layer by selecting the up arrow Checking the Simulation At this point, we have completely defined the MODFLOW data and we are ready to run the simulation. However, before saving the simulation and running MODFLOW, we should run the MODFLOW Model Checker one more time and check for other errors. Because of the significant amount of data required for a MODFLOW simulation, it is often easy to omit some of the required data or to define inconsistent or incompatible options and parameters. Such errors will either cause MODFLOW to crash or to generate an erroneous solution. The purpose of the Model Checker is to analyze the input data

114 7-24 GMS Tutorials currently defined for a MODFLOW simulation and report any obvious errors or potential problems. Running the Model Checker successfully does not guarantee that a solution will be correct. It simply serves as an initial check on the input data and can save a considerable amount of time that would otherwise be lost tracking down input errors. To run the Model Checker: 1. Select the Check Simulation command in the MODFLOW menu. 2. Select the Run Check button. A list of messages are shown for each of the MODFLOW input packages. If you have done everything correctly, there should be no errors for any of the packages but perhaps a few warnings. When there is a warning or an error, the Model Checker helps fix the problems. If you select or highlight one of the errors in the error list, a list of suggested steps for fixing the problem appears in the window at the bottom of the Model Checker. When appropriate, it also selects the cells or layers associated with the problem. The Model Checker can be left on the desktop while the steps are followed to fix the problem. The Model Checker operates differently than most other dialogs in GMS. It acts as a "modeless" dialog. This means that you do not have to exit the dialog to continue working with other functions within GMS. Once you think you have fixed the problem, the Run Check command can then immediately be executed again to ensure that the error has been fixed. Select the Done button to exit the Model Checker Saving the Project Now we are ready to save the project and run MODFLOW. 1. Select the Save As command in the File menu. 2. Enter "easttex" as the name of the model. 3. Select the Save button. Note: Saving the project not only saves the MODFLOW files but is saves all data associated with the project including the feature objects and scatter points. When running multiple versions of the MODFLOW simulation the Save/Save As commands in the MODFLOW menu can be used to save different versions of the MODFLOW simulation without saving the entire project.

115 MODFLOW - Conceptual Model Approach Running MODFLOW We are now ready to run MODFLOW. 1. Select the Run MODFLOW command from the MODFLOW menu. 2. Select the OK button. At this point MODFLOW is launched in a new window. MODFLOW opens the file and begins the simulation. As the simulation proceeds, you should see some text output in the window reporting the solution progress. When the solution is finished, close the window and return to GMS Viewing the Head Contours We are now ready to view the solution. 1. Select the Read Solution command from the MODFLOW menu. 2. Select the OK button. A set of contours should appear. To get better contrast between the contours and the background image, we will change the contour color to blue. 1. Select the Contour Options command in the Data menu. 2. Click on the Contour color window. 3. Select the Color button. 4. Select a dark blue color. 5. Select the OK button repeatedly to exit all dialogs. To view the contours for the second layer: 1. Select the down arrow in the mini-grid display. 2. After viewing the contours, return to the top layer by selecting the up arrow Viewing the Water Table in Side View Another interesting way to view a solution is in side view. 1. Select a cell somewhere near the well on the right side of the model.

116 7-26 GMS Tutorials 2. Select the View J Axis macro. Notice that the computed head values are used to plot a water table profile. Use the left and right arrow buttons in the mini-grid display to move back and forth through the grid. You should see a cone of depression at the well. When finished: Select the View K Axis macro Viewing the Flow Budget The MODFLOW solution consists of both a head file and a cell-by-cell flow (CCF) file. GMS can use the CCF file to display flow budget values. For example, we may want to know if any water exited from the drains. This can be accomplished simply by clicking on a drain arc. 1. Switch to the Map module. 2. Choose the Select Arcs tool. 3. Click on the rightmost drain arc. Notice that the total flux through the arc is displayed in the strip at the bottom of the window. Next, we will view the flux to the river. 1. Click on one of the specified head arcs at the bottom and view the flux. 2. Hold down the Shift key and select each of the specified head arcs. Notice that the total flux is shown for all selected arcs. These same steps can be used to display flux through polygons such as recharge polygons. Flux for a set of selected cells can be displayed as follows: 1. Switch to the 3D Grid module. 2. Select a group of cells by dragging a box around the cells. 3. Select the Flow Budget command from the Data menu. This dialog shows a comprehensive flow budget for the selected cells. 1. Select Done to exit the dialog. 2. Click anywhere outside the model to unselect the cells.

117 MODFLOW - Conceptual Model Approach Adding Annotation GMS includes a wide selection of tools for preparing graphical output to include in a final report of a modeling study. These options include printing, exporting DXF or TIFF files, and copying images to the clipboard. Before printing an image or copying the image into another document, it is often useful to add some annotation to the image in order to provide a title or highlight important features. Annotation can be added with the drawing tools provided in the Map module. For example, to place a label on a well: 1. Switch to the Map module. 2. Select the Create Text tool. 3. Click just above the well on the east (right) side. 4. Delete the default text string "text" and type "Well #2". 5. Select the Fill behind text option. 6. Select the OK button. To reposition the text: 1. Select the Select Drawing Objects tool. 2. Click on the text and drag it to a new location. To change the text: 1. Double click on the text. 2. Change the name to "Well 54A". 3. Select the OK button. To add a title to the drawing: 1. Select the Create Text tool. 2. Click in the top center of the Graphics Window, just above the model. 3. Enter "East Texas Groundwater Model" for the title. 4. Select the Fill behind text option.

118 7-28 GMS Tutorials 5. Select the Font button. 6. Change the font size to 18 pt. 7. Select the OK button to exit the Font dialog. 8. Select the OK button to exit the Text dialog. Sometimes it is useful to use both an arrow and a label to highlight a feature. 1. Click in the lower left corner of the window, a few centimeters below the bottom boundary of the model. 2. Enter "Lampasas River" for the text. 3. Select the Fill behind text option. 4. Select the OK button. 5. Select the Create Line tool. 6. Draw a line from the "Lampasas River" text to the lower model boundary by clicking near the text and then double clicking at the end of the line near the lower boundary. 7. Select the Select Drawing Objects tool. 8. Double click on the line you just created. 9. In the Arrowheads section, select the End option. 10. Select the OK button. 11. Click anywhere in window other than on a drawing object to unselect the arrow Conclusion This concludes the MODFLOW - Conceptual Model Approach tutorial. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

119 8 MODPATH CHAPTER 8 MODPATH This tutorial describes the steps involved in setting up a MODPATH simulation in GMS. MODPATH is a particle tracking code developed by the U.S. Geological Survey. MODPATH tracks the trajectory of a set of particles from user-defined starting locations using the MODFLOW solution as the flow field. The particles can be tracked either forward or backward in time. Particle tracking solutions have a variety of applications, including the determination of zones of influence for injection and extraction wells. 8.1 Description of Problem The problem we will be solving for this tutorial is an extension of the problem described in the previous tutorial entitled MODFLOW - Conceptual Model Approach. If you have not yet completed the previous tutorial, you may wish to do so before continuing. In the previous tutorial, a site in East Texas was modeled. We will be using the solution from this model as our flow field for the particle tracking simulation. The model includes a proposed landfill. For this tutorial, we will be performing two particle tracking simulations to analyze the long term effects of contamination from the landfill. In the first simulation, we will be performing reverse particle tracking from the well on the east side of the model to see if the zone of influence of the well overlaps the landfill. In the second simulation, we will be performing a forward tracking simulation using an array of particles starting at the landfill to analyze the region of potential contamination for the landfill.

120 8-2 GMS Tutorials 8.2 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state. 8.3 Required Modules/Interfaces This tutorial utilizes the following components of the GMS interface: The 3D Grid module The Map module The MODPATH interface. You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If you have licensed and enabled each of the listed items on your version of GMS, you can proceed to complete the tutorial in normal mode. If not, you will need to obtain an updated password or hardware lock before continuing. 8.4 Importing the Project The first step is to import the East Texas project. This will read in the MODFLOW model and solution, and all other files associated with the model. To import the project: 1. Select the Open command from the File menu. 2. In the Open dialog, locate and open the directory entitled tutorial\modfmap\sample. 3. Select the file entitled sample.gpr. 4. Choose the Open button. 8.5 Initializing the MODPATH Simulation Now that the MODFLOW model is in memory, we can initialize the MODPATH simulation.

121 MODPATH 8-3 Switch to the 3D Grid module. Select the New Simulation command from the MODPATH menu. 8.6 Assigning the Porosities In order to calculate the tracking times, a porosity must be defined for each of the cells in the grid. We will assign one porosity value to layer one and another to layer two. Porosities will be assigned to polygons in the conceptual model and then converted to the grid cells using the Map -> MODPATH command. 1. Switch to the Map Module. 2. In the Coverages combo box at the top of the GMS window, select the Layer 1 coverage. 3. Choose the Select Polygons Tool. 4. Double click on the layer polygon. 5. Turn on the Aquifer Porosity option and enter a value of 0.30 for the porosity. 6. Select the OK button. Next, we will assign a porosity value to layer In the Coverages combo box at the top of the GMS window, select the Layer 2 coverage. 2. Double click on the layer polygon. 3. Turn on the Aquifer Porosity option and enter a value of 0.40 for the porosity. 4. Select the OK button. 5. Click anywhere outside the model to unselect the highlighted polygon Assigning the Porosities to the Cells The last step in assigning the porosities is to convert the porosities defined at the polygons to cell-by-cell values.

122 8-4 GMS Tutorials 1. Select the Map -> MODPATH command in the Feature Objects menu. 2. Select OK at the prompt. 8.7 Defining the Starting Locations Next, we need to specify the starting locations for the particles. We will create a set of particle starting locations surrounding the cell containing the well on the east side of the model Selecting the Cell To assign the starting locations, we must first select the cell containing the well. To make sure we select the correct cell, we will zoom in on the model in the area of the well. 1. Switch to the 3D Grid module. 2. In the mini-grid display in the Tool Palette, select the down button to move to the second layer (the well is in the bottom layer). 3. Select the Zoom tool. 4. Click once on the location of the well on the right side of the model. This zooms the image by a factor of two around the point clicked. 5. Click multiple times if necessary until the cell containing the well is clearly distinguishable from the surrounding cells. To select the cell: 1. Select the Select Cells tool. 2. Click in the cell containing the well Creating the Starting Locations To generate the starting locations: 1. Choose the Generate Particles command from the MODPATH menu. 2. Select the Distribute starting points on cell faces option.

123 MODPATH For Face 1, change the number in the NZ field to 2. Do the same for Face 3, 2 and Select the OK button. A set of particles should appear around the perimeter of the cell. To restore the display: 1. Select the Frame macro. 2. Select the up arrow to return to layer one. 8.8 Specifying the Tracking Direction The last step in setting up the MODPATH data is to specify the tracking direction. Since we want to delineate the capture zone for the well, we will perform backward tracking and track the particles upgradient. 1. Select the General Options command from the MODPATH menu. 2. At the top of the dialog, select the Backward option. 3. Select the OK button. 8.9 Saving the Simulation We are now ready to save the simulation and run MODPATH. 1. Select the Save As command from the MODPATH menu. 2. In the Save File dialog, locate and open the directory entitled tutorial\modpath. 3. Enter path1.rsp for the file name. 4. Select the Save button Running MODPATH We are now ready to run MODPATH. To launch MODPATH: 1. Select the Run MODPATH command from the MODPATH menu. 2. Select the OK button.

124 8-6 GMS Tutorials At this point MODPATH is launched in a new window. The response file name is passed to MODPATH as a command line argument. MODPATH opens the file and begins the simulation. As the simulation proceeds, you should see some text output in the window reporting the solution progress. When the solution is finished, close the window and return to GMS Viewing the Solution To view the computed pathlines: 1. Select the Read Solution command from the MODPATH menu. 2. Select the OK button. You should see a set of pathlines which converge on the east well. Notice that the pathlines intersect the area covered by the proposed landfill, indicating a potential for leachate from the landfill to appear in the water pumped from the well Viewing the Pathlines in Cross Section View The 3D nature of the pathlines is best seen in cross section view. 1. Select a cell near the right landfill. 2. Select the View J Axis macro. You may wish to move back and forth through the columns. When finished: Select the View K Axis macro Tracking Particles from the Landfill Next, we will perform a second particle tracking simulation. This time we will perform forward tracking from a set of starting locations which coincide with the site of the proposed landfill Changing the Tracking Direction First, we will change the tracking direction to forward. 1. Select the General Options command from the MODPATH menu. 2. At the top of the dialog, select the Forward option.

125 MODPATH Select the OK button Deleting the Starting Locations Next, we will delete the starting locations that we created around the well. 1. Select the Select Starting Locations tool. 2. Select the particles by dragging a rectangle that surrounds the east well. 3. Delete the particles by selecting the Backspace key or selecting the Delete command from the Edit menu. 4. Select OK at the first prompt. 5. Select OK at the second prompt Defining the New Starting Locations Finally, we will create a new set of starting locations at the site of the proposed landfill. The particles will be placed on the top of the ground water table to simulate leachate entering from the surface. Before selecting the cells, we will make the recharge coverage the active coverage so that the landfill polygon is clearly visible. 1. In the Coverages combo box at the top of the window, select the Recharge coverage. To select the cells: 1. Select the Select Cells tool. 2. Select the cells covered by the landfill by dragging a rectangle that coincides precisely with the landfill boundary. 3. Select the Generate Particles command in the MODPATH menu. 4. Select the Distribute starting points on w.t. surface option. 5. Select the OK button. 6. Click anywhere outside the grid to unselect the cells.

126 8-8 GMS Tutorials 8.13 Saving the Simulation We are now ready to save the new simulation. 1. Select the Save As command in the MODPATH menu. 2. Change the file name to path2.rsp. 3. Select the Save button Running MODPATH Using the same steps you followed above, execute MODPATH and compute a solution with the path2.rsp response file Viewing the Solution To view the results from the second simulation: 1. Select the Read Solution command from the MODPATH menu. 2. Select the OK button. Now you should see a set of pathlines starting at the landfill and terminating in the well, the creek bed, and in the river at the bottom of the model. You may wish to view this solution in cross section view as well Conclusion This concludes the MODPATH tutorial. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

127 9 MT3DMS Grid Approach CHAPTER 9 MT3DMS - Grid Approach This tutorial describes how to perform an MT3DMS simulation within GMS. An MT3DMS model can be constructed in GMS using one of two approaches: the conceptual model approach or the grid approach. With the conceptual model approach, the sources/sinks and zones in the model are defined with GIS objects and automatically assigned to the grid. With the grid approach, values are manually assigned to the grid. While the conceptual model approach is generally preferable for large, complicated models, simple models can be easily constructed using the grid approach. The grid approach is described in this tutorial. The following tutorial describes the conceptual model approach. 9.1 Description of Problem The problem to be solved in this tutorial is shown in Figure This problem corresponds to the sixth sample problem ("Two-Dimensional Transport in a Heterogeneous Aquifer") described in the MT3DMS documentation. The problem consists of a low K zone inside a larger zone. The sides of the region are no flow boundaries. The top and bottom are constant head boundaries that cause the flow to move from the top to the bottom of the region. An injection well with a specified concentration provides the source of the contaminants. A pumping well serves to withdraw contaminated water migrating from the injection well. A steady state flow solution will be computed and a transient transport simulation will be performed over a one year period.

128 9-2 GMS Tutorials Constant head boundary (H=250 m) (flow model) No mass flux boundary (transport model) Hyd. Cond. = 1.474x10-7 m/s LOW K ZONE INJECTION WELL Q = m 3 /s C = ppm No flow boundary (flow model) No mass flux boundary (transport model) DY = 2000 m PUMPING WELL Q = m 3 /s Number of rows = 40 Number of columns = 32 Aquifer thickness = 10 m K = 1.474x10-4 m/s Porosity = 0.3 Longitudinal dispersivity = 20 m Dispersivity ratio = 0.2 Simulation time = 1.0 yr No flow boundary (flow model) No mass flux boundary (transport model) DX = 1600 m Constant head boundary (H = m) Figure 9.1 Sample Flow and Transport Problem. 9.2 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state. 9.3 Required Modules/Interfaces This tutorial utilizes the following components of the GMS interface: The 3D Grid module The MODFLOW interface The MT3DMS interface You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If you have licensed and enabled each of the listed items on your version of GMS,

129 MT3DMS - Grid Approach 9-3 you can proceed to complete the tutorial in normal mode. If not, you will need to obtain an updated password or hardware lock before continuing. The tutorial cannot be completed in demo mode because the ability to save files is required. 9.4 Building the Flow Model Before setting up the MT3DMS simulation, we must first create a MODFLOW simulation. The resulting MODFLOW solution will then be used as the flow field for the transport simulation. If you are already familiar with how to create a flow model and would like to skip this section, you can read in a flow model that has already been prepared. Otherwise, continue through section 9.4. To skip this section and read in a flow model that has already been prepared: 1. Select the Open command from the File menu. 2. Locate and open the directory entitled tutorial\mt3dgrid\sample. 3. Select the file entitled flowmod.mfs. 4. Choose the Open button. 5. Switch to the 3D Grid module. 6. Skip ahead to section Creating the Grid The first step in setting up the flow simulation is to create the grid. To create the grid: 1. Switch to the 3D Grid module. 2. Select the Create Grid command from the Grid menu. 3. In the section entitled X-dimension, enter for the Length value, and 32 for the Number Cells value. 4. In the section entitled Y-dimension, enter for the Length value, and 40 for the Number Cells value. 5. Select the OK button.

130 9-4 GMS Tutorials A grid should appear in the Graphics Window Initializing the MODFLOW Simulation To initialize a new MODFLOW simulation: Select the New Simulation command in the MODFLOW menu The Basic Package The next step in setting up the MODFLOW simulation is to initialize the data in the Basic package. Headings First, we will enter the headings and other basic information. 1. Select the Basic Package command from the MODFLOW menu. 2. For the first line of the heading, enter: "GMS MT3DMS Tutorial - MODFLOW Simulation". 3. For the second line of the heading, enter your name and the current date. Units Next, we will define the model units. 1. Select the Units button. 2. Select m for the Length unit. 3. Select d for the Time unit. 4. Select kg for the Mass unit. 5. Select ppm for the Concentration unit. 6. Select the OK button. Package Selection Next, we will select the packages we wish to use. 1. Select the Packages button. 2. Turn on the Well package.

131 MT3DMS - Grid Approach In the Solver section, select the Strongly Impl. Proc. (SIP1) option. 4. Select the OK button to exit the Packages dialog. The IBOUND Array The next step is to set up the IBOUND array. The IBOUND array is used to designate each cell as either active (IBOUND>0), inactive (IBOUND=0), or constant head (IBOUND<0). For our problem, all cells will be active, except for the top and bottom rows, which will be designated as constant head. The default value for the IBOUND array is active, thus, all we need to do is change the IBOUND value for the top and bottom rows to a value less than zero (-1). This could be accomplished with the IBOUND array editor that is accessed through the IBOUND button, but in this case, it is easier to select the cells in the Graphics Window and assign a value using the Cell Attributes dialog. 1. Select the Close button to exit the Basic Package dialog. 2. Choose the Select i tool in the Tool Palette. 3. Click anywhere in the top row to select it. 4. While holding down the Shift key, click anywhere in the bottom row. 5. Select the Cell Attributes command in the MODFLOW menu. 6. Enter a value of 1 for the IBOUND value. 7. Select the OK button. 8. Click outside the grid to unselect the cells. The Starting Head Array The next step is to set up the Starting Heads array. The Starting Heads array is used to establish an initial head value that MODFLOW will modify in an iterative fashion until the solution converges. Based on the boundary conditions for our problem, it is reasonable to expect that the heads will range from m to 250 m. We will assign a constant value for the starting head that is an average of these values. 1. Select the Basic Package command from the MODFLOW menu. 2. Select the Starting Heads button. 3. Select the Constant -> Grid button.

132 9-6 GMS Tutorials 4. Make sure the Apply to variable head cells only option is selected and select the OK button. 5. Enter a value of Select the OK button. 7. Select the OK button to exit the Starting Heads Array dialog. Constant Head Cells The starting head array is also used in conjunction with the IBOUND array to define constant head cells. The negative value in the IBOUND array for a cell marks the cell as a constant head cell but the head associated with the cell is entered in the Starting head array. Thus, we must enter the constant head values for the top and bottom rows in the starting head array. First, we will enter the linearly varying head values along the bottom row of the grid. The easiest way to assign these values is by selecting the cells directly in the Graphics Window. 1. Select the Close button to exit the Basic Package dialog. 2. With the Select i tool still active, click anywhere in the top row to select it. 3. Select the Cell Attributes command in the MODFLOW menu. 4. Enter a value of 250 for the Starting Head value. 5. Select the OK button. 6. Repeat steps 2-5 to assign a value of to the bottom row. This concludes the input for the Basic package The BCF Package The next step in setting up the model is to enter the data for the block-centered flow (BCF) package. 1. Select the BCF Package command from the MODFLOW menu. 2. In the Layer Type section, choose the Confined option. The buttons in the lower right portion of the dialog are for entering layer data. First, we will enter the top and bottom elevations. We will use a constant elevation throughout the grid. The bottom elevation is zero and top elevation

133 MT3DMS - Grid Approach 9-7 is ten meters. This happens to be the default values assigned to a new grid. Thus, in this case, we don t need to make any changes to the elevations. The next value to assign is the horizontal hydraulic conductivity (k). For our problem, the grid will have one k value except for one region, which will have a lower value. To enter the k values, we will first assign a global k value and then select the cells in the low k region and assign the values directly. To assign the global k value: 1. Select the Horizontal Hyd. Conductivity button. 2. Select the Constant to Grid button. 3. Enter a value of 12.7 (note:1.474e-3 m/s X 3600 s/hr X 24 hr/d = 12.7 m/d). 4. Select the OK and Close buttons repeatedly to exit all dialogs. Now we will select the cells in the low K zone to assign a lower value of K h. The low K zone extends from x=200 to x=900 in the horizontal direction and from y=1100 to y=1500 in the vertical direction. This corresponds to a rectangular region with the cell (11,5) in the upper left corner and the cell (18,18) in the lower right corner. To select the zone: 1. Select the Select Cells tool. 2. While examining the ijk display fields in the Edit Window, select the cell with I=11 and J=5. 3. While holding down the Shift key, select the cell with I=18 and J= Keep holding down the Shift key and drag a rectangle that just encloses the two cells you just selected. To assign the k value: 1. Select the Cell Attributes command in the MODFLOW menu. 2. Enter a value of in the Horizontal Hyd. Conductivity edit field (note: 1.474e-7m/s X 3600s/hr X 24hr/d = m/d). 3. Select the OK button Defining the Wells Finally, we will enter the data for the injection well and the pumping well. First, we will create the injection well. The well is located at the cell (10,16).

134 9-8 GMS Tutorials 1. Locate the cell in I=10 and J=16 and select it by clicking in the cell. 2. Select the Point Sources/Sinks command in the MODFLOW menu. 3. In the Well section, select the Add button. 4. Enter a value of 86.4 for the flow rate (note: 0.001m 3 /s X 3600s/hr X 24hr/d = 86.4m 3 /d). 5. Select the OK button. Next, we will create the pumping well. The well is located at the cell (24,16). 1. Locate the cell with I=24 and J=16 and select it. 2. Select the Point Sources/Sinks command in the MODFLOW menu. 6. In the Well section, select the Add button. 3. Enter a value of for the flow rate (note: m 3 /s X 3600s/hr X 24hr/d = m 3 /d). 4. Select the OK button Saving the Simulation We are now ready to save the simulation and run MODFLOW. 1. Select the Save As command from the MODFLOW menu. 2. In the Save dialog, locate and open the directory entitled tutorial\mt3dgrid. 3. Enter flow.mfs for the file name. 4. Select the Save button Running MODFLOW To run MODFLOW: 1. Select the Run MODFLOW command from the MODFLOW menu. 2. Select OK at the prompt. 3. When the simulation is finished, close the window and return to GMS.

135 MT3DMS - Grid Approach Viewing the Flow Solution Next, we will read in the computed head values for the flow model. 1. Select the Read Solution command from the MODFLOW menu. 2. Select OK button. 9.5 Building the Transport Model Now that the flow solution has been computed, we are ready to set up the MT3DMS transport simulation. Like MODFLOW, MT3DMS is structured in a modular fashion and uses a series of packages as input. Consequently, the GMS interface to MT3DMS is similar to the interface to MODFLOW and we will follow a similar sequence of steps to enter the input data Initializing the Simulation First, we will initialize the MT3DMS simulation. Select the New Simulation command from the MT3D menu The Basic Transport Package The MT3DMS Basic Transport package is similar to a combination of the MODFLOW Basic and BCF packages. It is always required and it defines basic information such as stress periods, active/inactive regions, and starting concentration values. Select the Basic Transport Package command from the MT3D menu. Headings To enter the headings: 1. For the first line of the heading, enter: "GMS MT3DMS Tutorial - MT3DMS Simulation". 2. For the second line of the heading, enter your name and the current date. Species Since MT3DMS is a multi-species model, we need to define the number of species and name each species. We will use one species named "tracer."

136 9-10 GMS Tutorials 1. Select the Define Species button. 2. Select the New button. 3. Change the name of the species to tracer. 4. Select the OK button to return to the Basic Transport Package dialog. Packages Next, we will select which packages we wish to use. 1. Select the Packages button. 2. Select the Advection Package option. 3. Select the Dispersion Package option. 4. Select the Source/Sink Mixing Package option. 5. Select the OK button to exit the Packages dialog. Stress Periods The next step is to set up the stress periods. The flow simulation was steady state but the transport simulation will be transient. We will run the simulation for a one year time period. To do this we will use a single stress period (since the input values are constant) and allow MT3DMS to determine the appropriate transport step size. 1. Select the Stress Periods button. 2. Change the Length field to Make sure the value in the Transport step size is zero. A value of zero signifies that MT3DMS will automatically compute the appropriate transport step size. 4. Select the OK button to exit the Stress Periods dialog. Output Control Next, we will specify the output options. 1. Select the Output Control button. 2. Select the Print or save at specified interval option.

137 MT3DMS - Grid Approach Change the specified interval to 10. This will output a solution at every tenth transport step. 4. Select the OK button to exit the Output Control dialog. ICBUND Array The ICBUND array is similar to the IBOUND array in MODFLOW. The ICBUND array is used to designate active transport cells (ICBUND>0), inactive transport cells (ICBUND=0), and constant concentration cells (ICBUND<0). In most problems, ICBUND will be similar to IBOUND but it will differ. Typically, the cells which are constant head cells in the flow solution are not constant concentration cells in the transport solution. For our problem, all of the cells are active, therefore, no changes are necessary. Starting Concentration Array The starting concentration array defines the initial condition for the contaminant concentration. In our problem, the starting concentrations are all zero and the default is adequate. HTOP and Thickness Arrays MT3DMS uses the HTOP array and a thickness array to determine the layer geometry. However, the values for these arrays are determined automatically from the MODFLOW layer data and no input is necessary. Porosity Array Finally, we will define the porosity for the cells. Our problem has a constant porosity of 0.3. This is the default value in GMS so no changes need to be made. This completes the definition of the Basic Transport package data. Select the Close button to exit the Basic Transport Package dialog The Advection Package The next step is to enter the data for the Advection package. 1. Select the Advection Package command from the MT3D menu. 2. For the Solution scheme, select the Third order TVD scheme (ULTIMATE) option. 3. Select the OK button.

138 9-12 GMS Tutorials The Dispersion Package Next, we will enter the data for the Dispersion package. 1. Select the Dispersion Package command from the MT3D menu. 2. Select the Longitudinal Dispersivity button. 3. Select the Constant -> Grid option. 4. Enter a value of Select the OK button. 6. Select the OK button to exit the Longitudinal Dispersivity dialog. 7. Enter a value of 0.2 for the Ratio of trans. dispersivity to long. dispersivity parameter. 8. Enter a value of 0.2 for the Ratio of vert. dispersivity to long. dispersivity parameter. 9. Select the Close button to exit the Dispersion Package dialog The Source/Sink Mixing Package Finally, we must define the data for the Source/Sink Mixing package. For our problem, we only have one source/sink: the injection well. To define the source at the injection well, we need to select the well and assign a concentration. 1. Select the cell containing the injection well (the upper well) by clicking anywhere in the interior of the cell. 2. Select the Point Sources/Sinks command in the MT3D menu. 3. Turn on the Well option. 4. Enter a value of for the concentration. 5. Select the OK button. 6. Click outside the grid to unselect the cell Saving the Simulation We are now ready to save the simulation and run MT3DMS.

139 MT3DMS - Grid Approach Select the Save As command from the MT3D menu. 2. Locate and open the directory entitled tutorial\mt3dgrid. 3. Enter trans.mts for the file name. 4. Select the Save button to save the files Running MT3DMS To run MT3DMS: 1. Select the Run MT3DMS command from the MT3D menu. 2. Select OK at the prompt. 3. When the simulation is finished, close the window and return to GMS Reading in the Transport Solution To read in the transport solution: 1. Select the Read Solution command from the MT3D menu. 2. Select the OK button Changing the Contouring Options When displaying plume data, the color fill option often provides excellent results. 1. Select the Contour Options command in the Data menu. 2. Turn on the Color fill between contours option. 3. Select the OK button Setting Up a Film Loop Finally, we will observe how the solution changes over the one year simulation by generating a film loop animation. To set up the film loop: 1. Select the Film Loop command in the Data menu. 2. Select the Setup button. 3. Turn on the Display clock option.

140 9-14 GMS Tutorials 4. Select the Use constant interval option and change the Time interval to This will result in 11 frames. 5. Select the OK button. You should see some images appear on the screen. These are the frames of the film loop which are being generated. When the filmloop is finished generating: 1. Select the Run button to begin the animation. 2. After viewing the animation, select the Stop button to stop the animation. 3. Select the Step button to move the animation one frame at a time. 4. You may wish to experiment with some of the other playback controls. When you are finished, select the Done button to exit the Film Loop dialog. 9.6 Conclusion This concludes the MT3DMS Grid Approach tutorial. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

141 10 MT3DMS Conceptual Model Approach CHAPTER 10 MT3DMS - Conceptual Model Approach MT3DMS simulations can be constructed using either the grid approach where data are entered on a cell-by-cell basis or using the conceptual model approach where the data are entered via points, arcs, and polygons. The previous tutorial described how to use the grid approach. This tutorial describes how to use the conceptual model approach Description of Problem The problem we will be solving for this tutorial is an extension of the problem described in the tutorial entitled MODFLOW - Conceptual Model Approach. Thus, if you have not yet completed the MODFLOW tutorial, you may wish to do so now before continuing. In the MODFLOW tutorial, a site in East Texas was modeled. We will be using the solution from this model as the flow field for the transport simulation. The model included a proposed landfill. For this tutorial, we will be performing two transport simulations to analyze the long term potential for migration of leachate from the landfill. In the first simulation, we will be modeling transport due to advection only. In the second simulation, we will include sorption and decay in addition to advection.

142 10-2 GMS Tutorials 10.2 Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state Required Modules/Interfaces This tutorial utilizes the following components of the GMS interface: The 3D Grid module The Map module The MT3DMS interface. You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If you have licensed and enabled each of the listed items on your version of GMS, you can proceed to complete the tutorial in normal mode. If not, you will need to obtain an updated password or hardware lock before continuing. The tutorial cannot be completed in demo mode because the ability to save files is required Importing the Project The first step is to import the East Texas project. This will read in the MODFLOW model and solution, the background image, and all other files associated with the model. To import the project: 1. Select the Open command from the File menu. 2. Locate and open the directory entitled tutorial\modfmap\sample. 3. Select the file entitled sample.gpr. 4. Choose the Open button.

143 MT3DMS - Conceptual Model Approach Initializing the MT3DMS Simulation Now that the MODFLOW model is in memory, we can initialize the MT3DMS simulation. First, we will initialize the model. 1. Switch to the 3D Grid module. 2. Select the New Simulation command from the MT3D menu. 3. Select the Basic Transport Package command from the MT3D menu Defining the Units First, we will define the units. We will not change the length and time units (these must be consistent with the flow model). However, we need to define units for mass and concentration. 1. Select the Units button. 2. Select slug for the Mass units. 3. Select ppm for the Concentration units. 4. Select the OK button Defining the Species Since MT3DMS is a multi-species model, we need to define the number of species and name each species. We will use one species named "leachate." 1. Select the Define Species button. 2. Change the name of the species to leachate. 3. Select the OK button to return to the Basic Transport Package dialog Defining the Stress Periods Next, we will define the stress periods. Select the Stress Periods button. Since the flow solution computed by MODFLOW is steady state, we are free to define any sequence of stress periods and time steps we wish. Since the leachate from the landfill will be released at a constant rate, we only need one stress period. We will enter the length of the stress period (i.e., the length of

144 10-4 GMS Tutorials the simulation) and let MT3DMS compute the appropriate transport time step length by leaving the transport step size at zero. 1. Enter for the stress period length (days). 2. Enter 2000 for the Max transport steps. 3. Select the OK button to exit the Stress Periods dialog Selecting Output Control By default, MT3DMS outputs a solution at every transport step. Since this results in a rather large output file, we will change the output so that a solution is written every time step (every 300 days). 1. Select the Output Control button. 2. Select the Print at specified times option. 3. Select the Times button. 4. Select the Initialize Values button 5. Enter the following values: Initial time step size: 300 Bias: 1.0 Maximum time step size: 300 Maximum simulation time: Select the OK or Close buttons three times to return to the Basic Transport Package dialog Selecting the Packages Next, we will specify which of the MT3DMS packages we intend to use. 1. Select the Packages button. 2. Select the Advection package, the Dispersion package, and the Source/Sink Mixing package options. 3. Select the OK button. Note that the Basic Transport Package dialog also includes some layer data. We will enter the data for these arrays at a latter point in the tutorial.

145 MT3DMS - Conceptual Model Approach 10-5 Select the Close button to exit the Basic Transport Package dialog Assigning the Aquifer Properties MT3DMS requires that a porosity and dispersion coefficient be defined for each of the cells in the grid. While these values can be assigned directly to the cells, it is sometimes convenient to assign the parameters using polygonal zones defined in the conceptual model. The parameters are converted to the grid cells using the Map -> MT3DMS command Assigning the Parameters to the Polygons To assign the porosities and dispersion coefficients to the polygons: 1. Switch to the Map Module. 2. In the Coverages combo box at the top of the GMS window, select the Layer 1 coverage. 3. Choose the Select Polygons tool. 4. Double click on the layer polygon. 5. Turn on the Aquifer Porosity option and enter a value of Turn on the Longitudinal dispersivity option and enter a value Select the OK button. To assign the values to layer 2: 1. In the Coverages combo box at the top of the GMS window, select the Layer 2 coverage. 2. Double click on the layer polygon. 3. Turn on the Aquifer Porosity option and enter a value of Turn on the Longitudinal dispersivity option and enter a value Select the OK button. 6. Click anywhere outside the model to unselect the highlighted polygon.

146 10-6 GMS Tutorials 10.7 Assigning the Recharge Concentration The purpose of our model is to simulate the transport of contaminants emitted from the landfill. When the flow model was constructed, a separate, reduced value of recharge was assigned to the landfill site. This recharge represents leachate from the landfill. We will assign a concentration to this recharge. The concentration can be assigned directly to the recharge polygon in the conceptual model. 1. In the Coverages combo box at the top of the GMS window, select the Recharge coverage. 2. Double click on the landfill polygon. 3. For the Contaminant concentration in the Recharge section at the top right of the dialog, enter a constant value of for the concentration. 4. Select the OK button. 5. Click anywhere outside the model to unselect the polygon Converting the Conceptual Model At this point, we are ready to assign the aquifer parameters and the recharge concentration to the cells using the conceptual model. 1. Select the Map -> MT3DMS command in the Feature Objects menu. 2. Make sure the "All applicable coverages" option is selected and select OK at the prompt Layer Thicknesses To define the aquifer geometry, MT3DMS requires an HTOP array defining the top elevations of the uppermost aquifer. A thickness array must then be entered for each layer. Since we used the "true layer" approach to build the MODFLOW model, the layer geometry is automatically generated and no further input is necessary The Advection Package Before running MODFLOW, there are a few more options to enter. First, we need to select a solver for the Advection package.

147 MT3DMS - Conceptual Model Approach Switch to the 3D Grid module. 2. Select the Advection Package command from the MT3D menu. 3. For the solution scheme, select the Method of Characteristics (MOC) option. 4. Select the OK button The Dispersion Package Next, we will enter the data for the Dispersion package. Select the Dispersion Package command from the MT3D menu. The longitudinal dispersivity values were automatically assigned from the conceptual model. All we need to do is specify the remaining three parameters. 1. Enter a value of 0.2 for the Ratio of transverse disp. to long. disp. parameter. 2. Enter a value of 0.2 for the Ratio of vert. disp. to long. disp. parameter. 3. Ensure that the value of the Effective molecular diff. coefficient is zero. 4. Select the up arrow at the top of the dialog to switch to layer Once again, enter 0.2 for both dispersivity ratios. 6. Select the OK button to exit the Dispersion Package dialog The Source/Sink Mixing Package Dialog Finally, we must define the data for the source/sink mixing package. However, the only data required in this package for our simulation are the concentrations assigned to the recharge from the landfill. These values were automatically assigned to the appropriate cells from the conceptual model. Thus, the input data for this package are complete.

148 10-8 GMS Tutorials Saving the Simulation We are now finished inputting the MT3DMS data and we are ready to save the model and run the simulation. To save the simulation: 1. Select the Save As command from the MT3D menu. 2. Locate and open the directory entitled tutorial\mt3dmap. 3. Enter run1.mts for the file name. 4. Select the Save button to save the files Running MT3DMS To run MT3DMS: 1. Select the Run MT3DMS command from the MT3D menu. 2. Select OK at the prompt. 3. When the simulation is finished, close the window and return to GMS Viewing the Solution We will now go back to GMS to view the solution computed by MT3DMS. 1. Select the Read Solution command from the MT3D menu. 2. Select the OK button. 3. In the TS combo box at the top of the window, select the last time step. It is often helpful to use the color filled contours option. To do this: 1. Select the Contour Options command in the Data menu. 2. Select the Contour specified range option. 3. Enter 1.0 for the minimum value and for the maximum. 4. Change the Contour Method to Color fill between contours. 5. Select the OK button to exit the Contour Options dialog.

149 MT3DMS - Conceptual Model Approach 10-9 You should now see a display of color shaded contours confined to the area adjacent to the landfill. Note that the leachate eventually reaches both the river and the well. To view the solution for layer two: Select the down arrow in the mini-grid display. To view the solution in cross section view: 1. Select the up arrow in the mini-grid display. 2. Select a cell in the vicinity of the landfill. 3. Select the View J Axis macro. 4. Use the left and right arrow keys to view the solution along different columns. 5. Select the View K Axis macro when finished Viewing a Film Loop Next, we will observe how the solution changes over the course of the simulation by generating a film loop animation. To set up the film loop: 1. Select the Film Loop command in the Data menu. 2. Select the Setup button. 3. Turn on the Display clock option. 4. Select the Use constant interval option. 5. Enter a value of for the Time interval. 6. Select the OK button. You should see some images appear on the screen. These are the frames of the film loop which are being generated. Once they are all generated you can play them back at a high speed. When the hourglass cursor disappears: 1. Select the Play button to begin the animation.

150 10-10 GMS Tutorials 2. After viewing the animation, select the Stop button to stop the animation. 3. Select the Step button to move the animation one frame at a time. 4. You may wish to experiment with some of the other playback controls. When you are finished, select the Done button to exit the Film Loop dialog Modeling Sorption and Decay The solution we have just computed can be thought of as a worst case scenario since we have neglected sorption and decay. Sorption will retard the movement of the plume and decay (due to biodegradation) will reduce the concentration. For the second part of the tutorial we will modify the model so that sorption and decay are simulated. We will then compare this solution with the first solution Turning on the Chemical Reactions Package Sorption and decay are simulated in the Chemical Reactions Package. We need to turn this package on before it can be used. 1. Select the Basic Transport Package command in the MT3D menu. 2. Select the Packages command. 3. Turn on the Chemical reaction package option. 4. Select the OK button to exit the Packages dialog. 5. Select the Close button to exit the Basic Transport Package dialog Entering the Sorption and Biodegradation Data Next, we will enter the sorption and biodegradation data in the Chemical Reactions Package dialog. 1. Select the Chemical Reaction Package command in the MT3D menu. 2. In the Sorption section, select the Linear isotherm option. 3. In the Kinetic rate reaction section, select the First-order irreversible kinetic reaction option.

151 MT3DMS - Conceptual Model Approach In the lower part of the dialog, enter the following values: Bulk density st sorption constant st order rate constant, dissolved phase st order rate constant, sorbed phase In both the middle and the bottom portion of the dialog, switch the layer to layer 2 and enter the following values: Bulk density st sorption constant st order rate constant, dissolved phase st order rate constant, sorbed phase Select the OK button to exit the dialog Saving the Simulation We are now ready to save the new simulation. 1. Select the Save As command in the MT3D menu. 2. Enter run2.mts for the file name. 3. Select the Save button Running MT3DMS Using the same steps you followed above, execute MT3DMS and compute a solution with the run2.mts super file Viewing the Solution To view the results from the second simulation: 1. Select the Read Solution command from the MT3D menu. 2. Select the OK button. 3. In the TS combo box at the top of the window, select the last time step. Notice that at the end of the simulation the plume is smaller and less advanced than in the first simulation.

152 10-12 GMS Tutorials Generating a Time History Plot A useful way to compare two transient solutions is to create an observation point and generate a time history plot Creating an Observation Coverage The first step in generating a time history plot is to create an observation coverage in the Map module. 1. Switch to the Map module. 2. Select the Coverages command in the Feature Objects menu. 3. Select the New button. 4. Enter "Obs. Pts." for the name of the coverage. 5. Change the type of the coverage to Observation. 6. Click on the Options button. 7. Select the New button. 8. Change the name to "concentration". 9. Select the OK button to exit the Observation Coverage Options dialog. 10. Select the OK button to exit the Coverages dialog Creating an Observation Point Next, we will create an observation point. 1. Select the Create Point tool. 2. While monitoring the cursor coordinates in the Edit Window, move the cursor to where the coordinates are approximately equal to (9365.0, ) and click once to create an observation point. 3. With the point still selected, select the Attributes command from the Feature Objects menu. 4. Select the Assign to specified layer option and select layer Select the OK button.

153 MT3DMS - Conceptual Model Approach Creating a Time Series Plot Next, we will create a time series plot: 1. Make sure the point you just created is still selected. 2. Select the Obs. Plot Options command in the Display menu. 3. Select the New button. 4. In the Plot type pull-down list, select the Time series option. 5. Select the OK button. Finally, to display the plot we must open the Plot Window. 1. Select the Show Plot Window command in the Display menu. 2. Select the Frame macro Plotting Multiple Curves By default, only the active data set is used to generate the time series plot. In many cases it is useful to plot the results from two simulations at once. To plot a curve for both solutions: 1. Select the Obs. Plot Options command in the Display menu. 2. Select the Options button. 3. Select the Use selected data set option. 4. Highlight the data set entitled leachate, the one turned off. 5. Select the Display toggle. 6. Select the OK button to exit the Time Series Plot Options dialog. 7. Select the OK button to exit the Observation Plot Options dialog Moving the Observation Point Once an observation point is created, it can be moved to a new location on the grid and the plot is automatically regenerated. 1. Select the Select Points/Nodes tool.

154 10-14 GMS Tutorials 2. Drag the point to a new location Conclusion This concludes the MT3DMS Conceptual Model Approach tutorial. If you wish to exit GMS at this time: 1. Select the Exit command from the File menu. 2. Select No at the prompt.

155 11 SEAM3D CHAPTER 11 SEAM3D SEAM3D is a reactive transport model used to simulate complex biodegradation problems involving multiple substrates and multiple electron acceptors. It is based on the MT3DMS code. In addition to the regular MT3DMS modules, SEAM3D includes a Biodegration package and NAPL Dissolution package. This tutorial illustrates how to use both of these packages to set up a reactive transport simulation Description of Problem The problem we will be solving in this tutorial is illustrated in Figure The site represents a shallow unconfined aquifer with a uniform flow field from left to right. A NAPL plume is located on the left side of the model. The NAPL plume contains two primary hydrocarbons, benzene and toluene. The benzene and toluene are dissolving into the ground water and are being transported to the right. We will set up a SEAM3D simulation that models the transport and sequential degradation of the contaminants via aerobic degradation and sulfate reduction over a 2000 day period. The model will include dispersion and retardation due to sorption. The reactions will be modeled using the Biodegradation package. The gradual release of contaminants from the NAPL plume will be modeled as a source term using the NAPL Dissolution package. For comparison purposes, the model will include a conservative (no sorption) and a non-conservative tracer.

156 11-2 GMS Tutorials 1000 ft LNAPL Plume Specified Head Boundary H = 22 ft 500 ft GW Flow Drain Elev = 7 ft Bottom elevation = 0 ft K = 50 ft/d Simulation time = 2000 d Figure 11.1 Problem to be Solved in SEAM3D Tutorial Getting Started If you have not yet done so, launch GMS. If you have already been using GMS, you may wish to select the New command from the File menu to ensure the program settings are restored to the default state Required Modules/Interfaces This tutorial utilizes the following components of the GMS interface: The 3D Grid module The Map module The SEAM3D interface. You can confirm whether each of these components has been enabled on your copy of GMS by selecting the Register command from the File menu. If you have licensed and enabled each of the listed items on your version of GMS, you can proceed to complete the tutorial in normal mode. If not, you will need to obtain an updated password or hardware lock before continuing. The tutorial cannot be completed in demo mode because the ability to save files is required.

157 SEAM3D Importing the Flow Model The first step in setting up the SEAM3D simulation is to import the MODFLOW flow model. A steady state flow model has been previously computed and is supplied with the tutorial files. 1. Switch to the 3D Grid Module. 2. Select the Read Simulation command in the MODFLOW menu. 3. In the Open dialog, locate and open the file entitled tutorial\seam3d\flowmod.mfs At this point, you should see a grid appear. To view the flow solution: 1. Select the Read Solution command in the MODFLOW menu. 2. Select OK at the prompt. A set of head contours should appear indicating a uniform flow field from left side to the right side Initializing the SEAM3D Simulation Before entering the SEAM3D data, we must first initialize the SEAM3D simulation. This allocates the memory and data structures used by GMS to set up a SEAM3D simulation. To initialize the simulation. Select the New Simulation command from the MT3D menu. The interface to MT3DMS, RT3D, and SEAM3D are all contained in the MT3D menu. Now that we have initialized the simulation, most of the menu commands in the MT3D menu are undimmed Basic Transport Package The next step is to enter the data required by the Basic Transport (BTN) package. The BTN package is used to set up the basic components of the simulation, including package selection, stress periods, and initial conditions. 1. Select the Basic Transport Package command from the MT3D menu. 2. In the Model section of the dialog select the SEAM3D option.

158 11-4 GMS Tutorials Defining the Units First of all, we will define the units. The length and time units will already be set by the MODFLOW model. We will specify the mass and concentration units. 1. Select the Units button. 2. Check to ensure that the length units are feet (ft) and the time units are days (d). 3. Change the mass units to milligrams (mg). 4. Change the concentration units to milligrams per liter (mg/l). 5. Select the OK button to exit the Units dialog. The units we have entered are for convenience only and do not affect the calculations. GMS displays these units next to the input fields to remind us of the proper units for each item. It is still up to the user to enter consistent units Setting up the Stress Periods The next step is to set up the stress periods. Since none of the sources change over the simulation, we can use a single stress period with a single time step of 2000 days. For the transport step size, we will use the default value of zero. This forces SEAM3D to compute the appropriate transport step size automatically. 1. Select the Stress Periods button. 2. Change the length of the stress period to Select the OK button to exit the Stress Periods dialog Package Selection Next, we will select the packages we will be using in the simulation. 1. Select the Packages button in the Basic Transport Package dialog. 2. Select the following packages: Advection Package Dispersion Package Source/Sink Mixing Package Chemical Reaction Package Biodegradation Package

159 SEAM3D 11-5 NAPL Dissolution Package. 3. Select the OK button to exit the Packages dialog Defining the Species Next, we will define the species used in the simulation. 1. Select the Define Species button. 2. Change the number of Nondegradable Tracers to Change the number of Hydrocarbon Substrates to In the Microbial Processes section of the dialog turn on the SO4 reduction option. 5. In the Products to track section of the dialog turn on the H2S option. Notice that as we make changes in the left side of the dialog, the species names are listed on the right side of the dialog. Some of these names are fixed, but some are user defined. We will supply more meaningful names to the tracers and hydrocarbons. 1. In the Names list, select the Tracer1 item and change the name to "Tracer (Conservative)." 2. Select the Tracer2 item and change the name to "Tracer (Non- Conservative)." 3. Select the Substrate1 item and change the name to "Benzene." 4. Select the Substrate2 item and change the name to "Toluene." 5. Select the OK button to exit the Define Species dialog Output Control We will now edit the Output Control data to specify how frequently the solution data should be saved for post-processing. We will save once every 100 days for a total of 20 data sets over the 2000 day simulation. 1. Select the Output Control button. 2. Select the Print at specified times option. 3. Select the Times button.

160 11-6 GMS Tutorials 4. Select the Initialize Values button. 5. Enter 100 for the Initial time step size. 6. Enter 100 for the Maximum time step size. 7. Enter 2000 for the Maximum simulation time. 8. Select the OK button to exit the Initialize Time Steps dialog. 9. Select the OK button to exit the Variable Time Steps dialog 10. Select the OK button to exit the Output Control dialog Entering the Porosity SEAM3D requires a porosity value for each cell in order to compute a correct seepage velocity for transport. We will use a constant porosity for the entire grid. To enter the porosity: 1. Select the Porosity button. 2. Select the Constant -> Grid button. 3. Enter a value of 0.25 and select OK. 4. Select the OK button to exit the Porosity dialog Starting Concentrations The mobile species are listed in the lower right corner of the BTN Package dialog. We must define a set of starting concentrations for each of the species. The default concentration is zero. This will be the correct starting concentration for the hydrocarbon substrates and the tracers. However, we must set the starting concentrations of the O2, SO4, and H2S to the correct background values. 1. Select O2 in the list and select the Starting Concentration button. 2. Select the Constant -> Grid button. 3. Enter a value of 4.0 (mg/l) and select the OK button. 4. Select the OK button to exit the Starting Concentration dialog. 5. Repeat this process to enter the following starting concentrations: S04 = 9.0 mg/l

161 SEAM3D 11-7 H2S = 0.01 mg/l This concludes the input for the BTN pacakge. Select the Close button to exit the Basic Transport Package dialog Advection Package Typically, the next step at this point would be to enter the data for the Advection package. However, the default solution scheme (Third Order TVD ULTIMATE) is adequate for this problem and no changes need to be made Dispersion Package Next, we will enter the data for the Dispersion package. The aquifer has a longitudinal dispersivity of 10.0 ft and a transverse (horizontal) dispersivity of 0.5 ft. The vertical dispersivity is assumed equal to the longitudinal dispersivity. 1. Select the Dispersion Package command in the MT3D menu. 2. Select the Longitudinal Dispersivity button. 3. Select the Constant -> Grid button. 4. Enter a value of 10.0 and select OK. 5. Select the OK button to exit the Longitudinal Dispersivity dialog. 6. Enter a value of 0.05 for the Ratio of the trans. dispersivity to long. dispersivity value. 7. Select the Close button to exit the Dispersion Package dialog 11.9 Source/Sink Mixing Package The next step is to enter the data for the Source/Sink Mixing package. This package is used to establish the concentration of water entering the system. For our problem, we have water entering the system on the left side of the model through the specified head boundary. We will enter the correct "background" concentrations for fresh water entering through this boundary. 1. Select the Select j tool.

162 11-8 GMS Tutorials 2. Select the leftmost column of cells. 3. Select the Point Sources/Sinks command from the MT3D menu. 4. Turn on the Constant head option. Once again, the default value is zero. That is the correct value for most of the species. We will change the value for O2, SO4, and H2S. 1. Select O2 from the text window containing the species names. 2. Enter a value of 4.0 in the Constant edit field. 3. Repeat this process to enter the following concentrations: S04 = 9.0 mg/l H2S = 0.01 mg/l 4. Select the OK button to exit the Point Sources/Sinks dialog Chemical Reaction Package Next, we will enter the data for the Chemical Reaction package. This package is the standard MT3DMS package that is used to simulate sorption and first order decay. The biodegradation reactions are simulated in the Biodegradation package that is unique to SEAM3D. We will use the Chemical Reaction package to simulation retardation due to sorption. 1. Select the Chemical Reaction Package command in the MT3D menu. 2. In the Sorption combo box, select the Linear isotherm option. 3. Enter a value of 5.0e7 for the Bulk density. The default sorption constant is zero. This is the correct value for the conservative tracer and for O2, SO4, and H2S. We will enter a non-zero value for the non-conservative tracer and for the two substrates. 1. Select Tracer (Non-Conservative) from the list. 2. Enter a value of 5.0e-9 for the 1st sorption constant. 3. Repeat steps 1-2 to enter the same value (5.0e-9) for Benzene and Toluene. 4. Select OK to exit the Chemical Reaction Package dialog.

163 SEAM3D NAPL Dissolution Package We are now ready to enter the data for the NAPL Dissolution package. For our problem we must simulate the gradual dissolution of contaminants from a plume into the groundwater. In MT3DMS, such a situation could be simulated using constant concentration cells, injection wells, or recharge. None of these options results in a realistic simulation of dissolution from a plume. The SEAM3D NAPL Dissolution package provides a more realistic representation of a contaminant plume. With this package, we identify the cells containing the plume and enter the initial concentration and dissolution rate for the contaminants. We also enter the initial mass fraction and solubility of each species in the plume. SEAM3D then simulates the release of the each of the species over duration of the simulation Selecting the Cells The first step is to select the cells where the plume is located. 1. Select the Select Cells tool. 2. Select the Find Cell command from the Grid menu. 3. Enter 9, 6, and 1 for the I, J, K value respectively and select OK. 4. Drag a rectangle to select a 4X2 rectangular region of cells as shown in Figure The currently selected cell represents the cell in the upper left corner of the grid of cells. Click here Drag to here Figure 11.2 Selecting the Cells Defining the Plume.